All other workflows
Workflow |
Description |
Topics |
Reporting |
Stars |
Watchers |
|---|---|---|---|---|---|
A benchmark dataset for data-driven weather forecasting |
dataset benchmark weather-forecast deep-learning |
last update 2024-01-01formatting: failedlinting: failed |
622 |
31 |
|
PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System |
snakemake energy energy-system power-systems energy-model pypsa energy-system-model energy-systems |
last update 2025-03-09formatting: passedlinting: failed |
399 |
18 |
|
ATLAS - Three commands to start analyzing your metagenome data |
metagenomics annotation snakemake assembly genomic-binning functional-annotation taxonomic-classifications |
last update 2024-12-17formatting: failedlinting: failed |
377 |
15 |
|
Bitextor generates translation memories from multilingual websites |
document-aligner apertium dictionaries crawler wget hunalign sentence-segmentation tokenizer bicleaner tmx warc corpus-tools corpus-processing corpus-generator parallel-corpora machine-translation neural-machine-translation statistical-machine-translation bitextor bleualign |
last update 2024-12-05formatting: failedlinting: failed |
292 |
30 |
|
PyPSA-Earth: A flexible Python-based open optimisation model to study energy system futures around t… |
pypsa-africa pypsa-earth energy-system-model python investment-optimization operational-optimization power-system-model scenario-analysis energy-system-planning power-system-planning |
last update 2025-03-09formatting: passedlinting: failed |
253 |
10 |
|
Fully reproducible, open source scientific articles in LaTeX. |
latex open-source reproducible-science continuous-integration reproducible-research scientific-papers scientific-workflows |
last update 2022-05-13formatting: failedlinting: failed |
227 |
5 |
|
The code, training pipeline, and models that power Firefox Translations |
machine-translation neural-machine-translation machine-learning ml |
last update 2025-03-07formatting: failedlinting: failed |
177 |
18 |
|
Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / … |
generalization memory-management pipeline spatial-omics spatial-transcriptomics snakemake spatialdata multiplexed-imaging |
last update 2025-03-10formatting: failedlinting: failed |
170 |
6 |
|
Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data |
rna-seq workflow |
last update 2024-12-06formatting: failedlinting: failed |
161 |
16 |
|
A SingleCell RNASeq pre-processing snakemake workflow |
drop-seq snakemake pipeline dropseq yaml star picard reference-genome umi scrbseq scrb-seq multiqc conda plot dropseqtools |
last update 2023-03-26formatting: failedlinting: failed |
136 |
8 |
|
Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis usi… |
rna-seq cdna differential-gene-expression differential-transcript-usage nanopore |
last update 2022-12-12formatting: failedlinting: failed |
92 |
21 |
|
Benchmarking analysis of data integration tools |
last update 2021-06-18formatting: failedlinting: failed |
92 |
13 |
||
Plotting tools for nanopore methylation data |
last update 2024-07-23formatting: failedlinting: failed |
89 |
9 |
||
Meta-pipeline to identify transposable element insertions using next generation sequencing data |
last update 2024-03-13formatting: failedlinting: failed |
85 |
15 |
||
A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and di… |
last update 2023-02-07formatting: failedlinting: failed |
82 |
8 |
||
Snakemake pipelines for nanopore sequencing data archiving and processing |
nanopore workflow snakemake-pipelines docker pipeline singularity |
last update 2022-02-16formatting: failedlinting: failed |
81 |
6 |
|
PyPSA-Eur-Sec: A Sector-Coupled Open Optimisation Model of the European Energy System |
pypsa energy energy-system energy-model energy-system-model |
last update 2023-07-04formatting: failedlinting: failed |
80 |
15 |
|
a snakemake pipeline to process ChIP-seq files from GEO or in-house |
chip-seq snakemake python |
last update 2021-04-30formatting: failedlinting: failed |
77 |
8 |
|
CADD scripts release for offline scoring. For more information about CADD, please visit our website |
last update 2024-12-10formatting: passedlinting: failed |
75 |
4 |
||
Scalable open-source software to run, develop, and benchmark causal discovery algorithms |
graphical-models bayesian-networks markov-networks benchmarking reproducible-research snakemake-workflow structure-learning causal-discovery causal-models causality |
last update 2025-03-06formatting: failedlinting: failed |
68 |
4 |
|
Snakemake pipeline that works with the scIB package to benchmark data integration methods. |
last update 2025-01-25formatting: failedlinting: failed |
68 |
7 |
||
Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metag… |
last update 2025-03-08formatting: failedlinting: failed |
63 |
5 |
||
🦠📇 Microbial genomes-to-report pipeline |
microbial-genomics snakemake genomes-to-report hpc conda apptainer bioinformatics pbs slurm bioconda prokaryotes metagenomics clinical-research archaea bacteria |
last update 2025-03-05formatting: failedlinting: failed |
56 |
2 |
|
Snakemake workflow for metagenomic classification with Kraken2 |
last update 2023-05-31formatting: failedlinting: failed |
54 |
4 |
||
Efficient implementatin of ESM family. |
esm protein protein-language-models |
last update 2025-01-27formatting: failedlinting: failed |
48 |
3 |
|
ATAC-seq snakemake pipeline |
atac-seq snakemake |
last update 2021-04-19formatting: failedlinting: failed |
48 |
5 |
|
Small collection of tools for performing quality control on coronavirus sequencing data and genomes |
last update 2024-06-30formatting: failedlinting: failed |
46 |
14 |
||
A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing |
last update 2021-08-16formatting: failedlinting: failed |
46 |
6 |
||
Amplicon sequence processing workflow using QIIME 2 and Snakemake |
noaa-omics-software amplicon-sequence-variants dada2 deblur snakemake |
last update 2025-02-18formatting: failedlinting: failed |
45 |
5 |
|
This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-through… |
last update 2024-12-11formatting: failedlinting: failed |
45 |
3 |
||
reproducible research project template for R using Renv and snakemake with an econ application |
snakemake snakemake-workflow economics workflow renv reproducible-research reproducibility |
last update 2022-08-02formatting: failedlinting: failed |
43 |
2 |
|
Improved structural variant discovery in accurate long reads using sample-specific strings (SFS) |
last update 2024-07-30formatting: passedlinting: failed |
42 |
4 |
||
MrBiomics: Modules & Recipes augment Bioinformatics for Multi-Omics Analyses |
automation bioinformatics biomedical data-science framework snakemake workflows epigenetics genetics genomics modules next-generation-sequencing python r recipes research science |
last update 2024-12-16formatting: failedlinting: failed |
41 |
5 |
|
No description available. |
last update 2022-10-22formatting: failedlinting: failed |
39 |
5 |
||
Ley Lab MetaGenome Profiler DataBase generator |
metagenomics ngs pipeline database |
last update 2022-12-04formatting: failedlinting: failed |
39 |
6 |
|
Bacterial GWAS analysis |
last update 2025-03-04formatting: failedlinting: failed |
37 |
2 |
||
🍄 Qiime2 ITS classifiers for the UNITE database |
last update 2025-03-09formatting: failedlinting: passed |
36 |
3 |
||
A template repository for snakemake workflows. |
last update 2024-11-23formatting: passedlinting: passed |
35 |
2 |
||
Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organis… |
last update 2023-12-29formatting: failedlinting: failed |
32 |
8 |
||
Explore the impacts of 24/7 Carbon-Free Energy PPAs |
energy energy-model power-system pypsa snakemake |
last update 2025-01-29formatting: failedlinting: failed |
31 |
2 |
|
Deep mutational scanning of the receptor-binding domain of SARS-CoV-2 Spike |
last update 2022-06-15formatting: failedlinting: failed |
31 |
3 |
||
A workflow and scripts for large-scale antiSMASH analyses |
last update 2024-11-05formatting: failedlinting: failed |
30 |
2 |
||
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of CO… |
virology sequencing biochemistry bioinformatics metagenomics |
last update 2024-07-23formatting: failedlinting: failed |
30 |
14 |
|
Analysis of imbalanced data and its impacts in a scRNA-seq integration setting |
last update 2024-12-11formatting: failedlinting: failed |
29 |
2 |
||
Open-source bioinformatics pipeline for the preprocessing of raw sequencing data. |
last update 2023-01-18formatting: failedlinting: failed |
27 |
5 |
||
No description available. |
last update 2023-03-09formatting: failedlinting: failed |
27 |
21 |
||
No description available. |
last update 2025-02-07formatting: failedlinting: failed |
25 |
4 |
||
Tumour-only somatic mutation calling using long reads |
last update 2024-12-12formatting: failedlinting: failed |
25 |
1 |
||
Extract lineage CSVs from NCBI for use with sourmash lca. |
last update 2023-10-04formatting: failedlinting: failed |
25 |
4 |
||
Untargeted metabolomics workflow for large-scale data processing and analysis implemented in Snakema… |
last update 2024-12-02formatting: failedlinting: passed |
24 |
6 |
||
Use an ensemble of variant callers to call variants from ATAC-seq data |
random-forest machine-learning snakemake atac-seq-data variant-calling |
last update 2025-03-05formatting: failedlinting: failed |
23 |
2 |
|
Snakemake pipeline calculating KEGG orthologue abundance in metagenomic sequence data. |
last update 2024-02-26formatting: failedlinting: failed |
23 |
3 |
||
A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spo… |
aws bioinformatics bioinformatics-pipeline ec2 ngs snakemake wgs giab ephemeral scaling budgeting genomic-data-analysis human-genome informatics parallel-cluster scalable slurm snv-call cwl |
last update 2025-03-09formatting: failedlinting: failed |
22 |
6 |
|
Harmonization of AMR predictor tool outputs |
antimicrobial-resistance standardization file-format |
last update 2025-01-14formatting: failedlinting: failed |
22 |
10 |
|
A pipeline for for large-scale analysis of antimicrobial resistance genes and their flanking regions… |
argprofiler |
last update 2025-01-16formatting: failedlinting: failed |
22 |
3 |
|
IRIS: Isoform peptides from RNA splicing for Immunotherapy target Screening |
immunotherapy rna-splicing neoantigen tumor-antigen rna-seq |
last update 2024-08-15formatting: failedlinting: failed |
22 |
7 |
|
Ancient microbiome snakemake workflow |
last update 2024-12-17formatting: failedlinting: failed |
21 |
9 |
||
Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | All… |
assemblies bacteria bioinformatics compression genomes indexing k-mers mof phylogenetic-compression phylogeny prophyle |
last update 2024-12-06formatting: passedlinting: failed |
21 |
7 |
|
A workflow for creating small NGS test data sets, useful for continuous integration. |
snakemake snakemake-workflows ngs |
last update 2024-08-15formatting: failedlinting: failed |
21 |
4 |
|
snakemake pipeline for Hi-C post-processing |
workflow snakemake analysis hi-c |
last update 2024-06-27formatting: failedlinting: failed |
21 |
4 |
|
Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search) |
assemblies bacteria bioinformatics compression genomes indexing k-mers mof phylogenetic-compression phylogeny |
last update 2024-05-22formatting: passedlinting: failed |
21 |
6 |
|
No description available. |
last update 2025-03-05formatting: passedlinting: failed |
20 |
4 |
||
Pipeline to run scE2G |
last update 2025-03-01formatting: failedlinting: failed |
20 |
4 |
||
Workflow for identifying and classifying homologous gene/protein sequences |
bioinformatics hmmer3 biopython python3 blast genome-annotation similarity-search coulson-plot transcriptome-annotation snakemake-workflow comparative-genomics homology molecular-evolution gene-families protein-families orthology |
last update 2025-01-16formatting: failedlinting: failed |
20 |
2 |
|
A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WG… |
pipeline genomics nvidia-clara-parabricks nvidia-gpu snakemake-pipeline gatk4 gatk-bestpractices illumina exome-pipeline cohort-analysis |
last update 2023-03-10formatting: failedlinting: failed |
20 |
5 |
|
PyPSA-DE: High resolution, sector-coupled model of the German Energy System |
last update 2025-03-04formatting: passedlinting: failed |
19 |
4 |
||
Plant genome assembly and annotation pipeline using snakemake |
last update 2023-05-17formatting: failedlinting: failed |
19 |
2 |
||
Education4Climate is a tool for crawling and analyzing data from higher education schools. |
last update 2025-02-26formatting: failedlinting: failed |
18 |
1 |
||
Clinical Whole Genome and Exome Sequencing Pipeline |
copy-number-variation germline-variants quality-control structural-variants singularity snakemake whole-genome-sequencing somatic-variants pipeline hla-typing variant-annotation variant-effect-prediction whole-exome-sequencing |
last update 2025-01-21formatting: failedlinting: failed |
18 |
1 |
|
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from… |
snakemake-workflow rna-seq variant-calling differential-expression population-genomics snakemake transcriptomics workflow population-genetics selection karyotype ancestry genomic-surveillance |
last update 2024-12-13formatting: failedlinting: failed |
18 |
2 |
|
Pipeline for Somatic Variant Calling with WES and WGS data |
snakemake bioinformatics somatic-variants exome-sequencing |
last update 2024-07-01formatting: failedlinting: failed |
18 |
4 |
|
Research pipeline for exploring clinically relevant genomic variants |
last update 2025-01-30formatting: failedlinting: failed |
17 |
7 |
||
Pipeline for Cut&Tag analysis |
last update 2025-01-16formatting: failedlinting: failed |
17 |
5 |
||
ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipelin… |
last update 2022-03-13formatting: failedlinting: passed |
17 |
2 |
||
Snakemake skeleton - Build workflows with Snakemake |
snakemake tutorial workflow skeleton |
last update 2024-05-17formatting: passedlinting: failed |
16 |
7 |
|
No description available. |
last update 2024-04-02formatting: failedlinting: failed |
16 |
26 |
||
RNAseq pipeline based on snakemake |
rnaseq snakemake |
last update 2023-03-15formatting: failedlinting: failed |
16 |
2 |
|
StaG Metagenomic Workflow Collaboration |
snakemake-workflows metagenomic-analysis metagenomics research microbiome |
last update 2021-04-13formatting: failedlinting: failed |
16 |
6 |
|
Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set |
r bioinformatics-pipeline reproducible-research rna-seq chip-seq bioconductor |
last update 2020-05-28formatting: failedlinting: failed |
16 |
2 |
|
A metatranscriptomic pipeline optimized for the study of microeukaryotes. |
last update 2024-11-22formatting: failedlinting: failed |
15 |
5 |
||
A Snakemake workflow for calling Fiber-seq Inferred Regulatory Elements (FIREs) on single molecules. |
last update 2024-12-08formatting: passedlinting: failed |
15 |
3 |
||
No description available. |
last update 2024-08-01formatting: failedlinting: failed |
15 |
1 |
||
Nextstrain build for avian influenza viruses |
nextstrain pathogen |
last update 2024-07-23formatting: failedlinting: failed |
15 |
18 |
|
Snakemake workflow to detect and classify viruses in metagenome assemblies. |
last update 2024-04-03formatting: failedlinting: failed |
15 |
1 |
||
Reproducible workflow for SARS-CoV-2 recombinant sequence detection. |
sars-cov-2 recombination recombinant genomics ncov |
last update 2023-02-09formatting: failedlinting: failed |
15 |
3 |
|
A workflow to build models of the European electricity system for Calliope. |
calliope-models conda europe research energy renewable-energy |
last update 2021-08-04formatting: failedlinting: failed |
15 |
6 |
|
No description available. |
last update 2021-05-07formatting: failedlinting: failed |
15 |
0 |
||
Signaling Pathway Reconstruction Analysis Streamliner (SPRAS) |
workkflow snakemake network omics |
last update 2025-03-07formatting: failedlinting: failed |
14 |
6 |
|
package to generate relative rotational positions and orientations of two molecular structures |
last update 2025-02-28formatting: failedlinting: failed |
14 |
1 |
||
CADD-SV – a framework to score the effect of structural variants |
sv variant-annotations variant-effect-prediction |
last update 2025-01-29formatting: failedlinting: failed |
14 |
4 |
|
Benchmarking computational methods for single-cell ATAC-seq and CUT&Tag |
last update 2024-08-22formatting: failedlinting: failed |
14 |
1 |
||
This exercise is the first part of the FAIR data reproducible projects pizza course, where we reprod… |
last update 2024-07-03formatting: failedlinting: failed |
14 |
4 |
||
A model that optimises investment and operation, and incorporates flexibility domestic demand flexib… |
energy energy-transition great-britain modelling open-source optimization python sector-coupling snakemake-workflow demand-flexibility energy-model energy-system-model power-systems pypsa |
last update 2024-03-05formatting: failedlinting: failed |
14 |
2 |
|
Sparse Signaling Pathway Sampling: MCMC for signaling pathway inference |
dynamic-bayesian-network gen probabilistic-programming signaling-pathway |
last update 2022-10-23formatting: failedlinting: failed |
14 |
4 |
|
Class materials for the NIH HPC snakemake class |
last update 2022-06-07formatting: failedlinting: failed |
14 |
7 |
||
Workflow for Nanopore Sequencing of 10x single cell libraries |
last update 2022-03-27formatting: failedlinting: failed |
14 |
4 |
||
Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DN… |
last update 2021-02-26formatting: failedlinting: failed |
14 |
4 |
||
A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(… |
last update 2021-01-14formatting: failedlinting: failed |
14 |
5 |
||
Pipeline for de novo clustering of long transcriptomic reads |
cdna rna-seq rna transcriptomics |
last update 2021-05-03formatting: failedlinting: failed |
14 |
23 |
|
Snakemake workflow for comparing E-G links to experimental data |
last update 2025-01-28formatting: failedlinting: failed |
13 |
5 |
||
3DGB is a workflow to build 3D models of genomes from HiC data |
hic 3d-genome vizualization |
last update 2024-09-19formatting: failedlinting: failed |
13 |
3 |
|
Snakemake workflow to systematically analyze BGCs and pangenomes of large number genomes |
pangenome-pipeline biosynthetic-gene-clusters genome-annotation genome-analysis |
last update 2023-07-07formatting: failedlinting: failed |
13 |
2 |
|
Open-source bioinformatics pipeline for the preprocessing of raw amplicon sequencing / metabarcoding… |
last update 2024-12-17formatting: failedlinting: failed |
12 |
1 |
||
Analysis code for Olink CVD1 - HF analysis |
last update 2024-08-14formatting: failedlinting: failed |
12 |
2 |
||
A pipeline for lightweight screening of Eukaryotic genomes and transcriptomes for recent HGT |
last update 2024-08-18formatting: failedlinting: failed |
12 |
5 |
||
Snakemake pipeline for 16S, 18S and ITS metagenomics using qiime2 |
conda microbiome picrust2 qiime2 |
last update 2024-03-01formatting: failedlinting: failed |
12 |
1 |
|
Snakemake workflow for comparison of differential abundance ranks |
bioinformatics workflow differential-abundance machine-learning metagenomics microbiome pipeline snakemake |
last update 2023-11-22formatting: failedlinting: passed |
12 |
5 |
|
shotgun pipeline |
last update 2020-05-01formatting: failedlinting: failed |
12 |
17 |
||
Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks in… |
last update 2021-02-19formatting: failedlinting: failed |
12 |
1 |
||
SigMa is a probabilistic model for the sequential dependencies of mutation signatures |
mutational-signatures hidden-markov-models cancer breast-cancer |
last update 2020-07-30formatting: failedlinting: failed |
12 |
7 |
|
A microbial genomic analysis pipeline used by the Djordjevic Lab |
last update 2025-02-09formatting: failedlinting: failed |
11 |
3 |
||
16S pipeline using qiime2 created with snakemake |
last update 2025-01-22formatting: passedlinting: passed |
11 |
1 |
||
Snakemake-based computational workflow for neoantigen prediction from diverse sources |
epitope gene-fusion indels neoantigens peptide snakemake snakemake-workflow splicing exitron neoepitope |
last update 2024-09-02formatting: failedlinting: failed |
11 |
3 |
|
Spliced peptide identification from in vitro digestions of polypeptides with purified proteasomes |
last update 2024-06-28formatting: failedlinting: failed |
11 |
2 |
||
Teaching materials for SymbNET course: from MAGs to GEMs |
metabolic modeling genome models metagenome assembled genomes symbnet metagem metabolism |
last update 2024-01-15formatting: failedlinting: failed |
11 |
1 |
|
Cell cycle analysis of single-cell proteomic and transcriptomic data for the FUCCI cell model |
last update 2023-08-05formatting: failedlinting: failed |
11 |
2 |
||
No description available. |
last update 2022-11-23formatting: failedlinting: failed |
11 |
3 |
||
A snakemake workflow for metagenomic projects |
metagenomics snakemake workflow assembly |
last update 2023-02-11formatting: failedlinting: failed |
11 |
34 |
|
Snakemake workflow for neoantigen prediction |
last update 2023-02-07formatting: failedlinting: failed |
11 |
4 |
||
:snake: Python framework for Nek5000 :rocket: |
python nek5000 snek5000 fluidsim snakemake jinja2 fluiddyn cfd simulation closember workflow |
last update 2022-10-27formatting: passedlinting: failed |
11 |
4 |
|
Estimation of solar and wind power generation potentials in Europe. |
renewable-energy electricity snakemake europe analysis reproducible-research |
last update 2022-07-02formatting: failedlinting: failed |
11 |
3 |
|
snakemake workflow for post-processing scATACseq data |
last update 2020-08-12formatting: failedlinting: failed |
11 |
0 |
||
A snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial … |
last update 2025-03-06formatting: failedlinting: failed |
10 |
5 |
||
A comprehensive quality-control and quantification RNA-seq pipeline |
rna-seq singularity quality-control gene-expression gene-fusions snakemake-pipeline |
last update 2025-03-06formatting: failedlinting: failed |
10 |
4 |
|
snakemake workflow for bulk RNA-seq workflow using STAR-edgeR |
snakemake rnaseq pipeline |
last update 2025-02-04formatting: failedlinting: failed |
10 |
4 |
|
Find endogenous viral elements in genomes |
last update 2025-02-06formatting: failedlinting: failed |
10 |
3 |
||
No description available. |
last update 2025-01-13formatting: failedlinting: failed |
10 |
3 |
||
A Snakemake-workflow to sample taxa from sequence databases based on taxonomical or phylogenetic inf… |
bioinformatics-pipeline phylogenomics |
last update 2025-01-19formatting: failedlinting: failed |
10 |
2 |
|
Snakemake module for the snpArcher pipeline for population size change inference. |
last update 2024-12-17formatting: failedlinting: failed |
10 |
1 |
||
Demographic analysis of Brassica oleracea |
last update 2024-11-08formatting: failedlinting: failed |
10 |
1 |
||
A Snakemake workflow for recovery of plastid genomes from metagenomic samples |
last update 2024-11-16formatting: failedlinting: failed |
10 |
3 |
||
Automated pipeline for amplicon sequence analysis |
amplicon-sequence-analysis snakemake illumina-sequencing pipeline otu-table |
last update 2024-12-04formatting: failedlinting: failed |
10 |
2 |
|
No description available. |
last update 2024-11-28formatting: failedlinting: failed |
10 |
4 |
||
We present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and hig… |
ribosome-profiling prokaryotes snakemake bioinformatics |
last update 2024-08-01formatting: failedlinting: failed |
10 |
5 |
|
No description available. |
last update 2024-08-09formatting: failedlinting: failed |
10 |
0 |
||
A repo for the Twist HiFi capture/snakemake workflow |
last update 2023-12-18formatting: failedlinting: failed |
10 |
14 |
||
🗺️ MAPP is a computational method which enables identification of binding motifs for RNA-binding pro… |
bioinformatics rna-seq splicing polyadenylation bioinformatics-pipeline computational-biology snakemake workflow |
last update 2024-05-21formatting: failedlinting: failed |
10 |
2 |
|
Extension of PyPSA-Eur to accomodate the computation and intersection of near-optimal feasible space… |
last update 2024-01-26formatting: failedlinting: failed |
10 |
4 |
||
Mutational antigenic profiling of SARS-CoV-2 RBD against human convalescent sera from the HAARVI coh… |
last update 2022-06-10formatting: failedlinting: failed |
10 |
4 |
||
Sector coupled Euro-Calliope workflow |
last update 2022-09-07formatting: failedlinting: failed |
10 |
3 |
||
Analysis code for the TAP-seq manuscript. |
last update 2021-06-25formatting: failedlinting: failed |
10 |
0 |
||
Recovery of prokaryotic genomes from shotgun metagenomic sequencing data |
last update 2021-04-19formatting: failedlinting: failed |
10 |
2 |
||
Code for the paper Spatio-temporal load shifting for truly clean computing |
energy power-systems pypsa snakemake |
last update 2025-02-04formatting: failedlinting: failed |
9 |
1 |
|
Analaysis for the batch correction paper |
last update 2025-01-13formatting: failedlinting: failed |
9 |
2 |
||
Code for the paper on 247-CFE procurement |
last update 2024-12-18formatting: failedlinting: failed |
9 |
1 |
||
Bioinformatics pipeline for the analysis of amplicon sequencing data of eDNA samples from the PacMAN… |
last update 2024-11-09formatting: failedlinting: failed |
9 |
7 |
||
This is a phylogeny workflow for batch submission to HPC cluster built with Slurm queue manager |
last update 2023-12-09formatting: failedlinting: failed |
9 |
3 |
||
Snakemake workflow to map and quantify microbial genomes in metagenomic reads |
last update 2024-02-28formatting: failedlinting: failed |
9 |
1 |
||
A scalable machine learning pipeline for probe specificity prediction. |
last update 2024-01-23formatting: failedlinting: failed |
9 |
4 |
||
No description available. |
last update 2023-12-18formatting: failedlinting: failed |
9 |
1 |
||
No description available. |
last update 2023-12-23formatting: failedlinting: failed |
9 |
1 |
||
Alignment and antibody assembly pipelines for Croote et al. (Science, 2018) |
last update 2021-08-15formatting: failedlinting: failed |
9 |
3 |
||
Is your European region able to provide itself with 100% renewable electricity? |
research renewable-energy paper europe analysis electricity-autarky reproducible-research |
last update 2021-07-19formatting: failedlinting: failed |
9 |
3 |
|
snakemake rules for running anvio |
last update 2021-01-14formatting: failedlinting: failed |
9 |
2 |
||
Repo to analyze population genetic data with many different methods |
population-genetics data-visualization principle-component-analysis structure admixture snakemake-workflow |
last update 2020-10-27formatting: failedlinting: failed |
9 |
5 |
|
Démonstration d’outils de bioinfo dans le cadre d’un projet |
last update 2020-12-16formatting: failedlinting: failed |
9 |
3 |
||
Using RNA-Seq data to improve microRNA target prediction accuracy in animals |
mirna-targets mirna mirna-mrna-interaction |
last update 2025-03-09formatting: failedlinting: failed |
8 |
2 |
|
Analysis for the second consortium paper. |
last update 2025-02-20formatting: failedlinting: failed |
8 |
9 |
||
The scripts contained in this repository were used for processing, analyzing, and visualizing TEQUIL… |
last update 2025-02-12formatting: failedlinting: failed |
8 |
6 |
||
No description available. |
last update 2025-01-09formatting: failedlinting: failed |
8 |
2 |
||
artempronozin95/ICAnnoLncRNA-identification-classification-and-annotation-of-LncRNA |
No description available. |
last update 2024-12-02formatting: failedlinting: failed |
8 |
1 |
|
Snakemake workflow for the vg toolkit. |
last update 2024-09-04formatting: failedlinting: failed |
8 |
10 |
||
Example project we use in the reproducibility lesson. |
last update 2024-09-19formatting: failedlinting: failed |
8 |
4 |
||
Ready-to-use pipeline to detect, count and identify the hgcAB genes, involved in mercury methylation… |
last update 2024-05-30formatting: failedlinting: failed |
8 |
3 |
||
Benchmarking adapter and quality trimming tools |
last update 2024-04-13formatting: failedlinting: failed |
8 |
3 |
||
Pharmacogenomics pipeline |
last update 2024-04-06formatting: failedlinting: failed |
8 |
8 |
||
Snakemake workflow to screen a set of genomes (e.g., MAGs) against an existing genome database and i… |
last update 2024-02-28formatting: failedlinting: failed |
8 |
1 |
||
Genome Assembly Validation via Inter-SUNK distances in ONT reads |
last update 2023-02-20formatting: failedlinting: passed |
8 |
2 |
||
PyPSA Model of the South African Energy System |
last update 2022-06-25formatting: failedlinting: failed |
8 |
8 |
||
Deep learning model for predicting environmental variables on river systems |
last update 2021-12-13formatting: failedlinting: failed |
8 |
8 |
||
uORF-Tools are a workflow and a collection of tools for the analysis of ‘Upstream Open Reading Frame… |
bioinformatics high-throughput-sequencing snakemake ribosome-profiling |
last update 2021-03-24formatting: failedlinting: failed |
8 |
2 |
|
Modular snakemake workflow for assembly-based metagenomics |
last update 2021-01-16formatting: failedlinting: failed |
8 |
3 |
||
Clin-mNGS: Automated pipeline for pathogen detection from clinical metagenomic data |
last update 2021-03-01formatting: failedlinting: failed |
8 |
1 |
||
Code for extracting parallel corpora from pmindia |
last update 2020-08-16formatting: failedlinting: failed |
8 |
1 |
||
Bioinformatics pipeline for nanopore sequencing data |
snakemake-workflows nanopore-sequencing bioinformatics-pipeline bacterial-genomes |
last update 2021-03-18formatting: failedlinting: failed |
8 |
3 |
|
Finding cryptic relationships to boost disease gene detection |
ibd-segments vcf estimate-relationships pipeline |
last update 2021-01-09formatting: failedlinting: failed |
8 |
9 |
|
Example of a snakemake workflow implementation of the mothur MiSEQ SOP |
last update 2021-02-10formatting: failedlinting: failed |
8 |
4 |
||
script to convert phewascatalog database to JSONs, with ENSGIDs and EFO ids. |
last update 2025-02-27formatting: failedlinting: failed |
7 |
11 |
||
Enhancer-Gene Prediction Pipeline based on logistic regression and ABC model |
last update 2025-02-09formatting: failedlinting: failed |
7 |
3 |
||
Snakemake workflow to analyze bulk RNA-seq |
last update 2024-12-18formatting: failedlinting: failed |
7 |
2 |
||
This is a pipeline for exploring viruses (ssDNA, dsDNA phage, and giant DNA viruses) and viral diver… |
bcbb-training metagenomics virus bioinformatics |
last update 2024-11-20formatting: failedlinting: failed |
7 |
5 |
|
Generation of OrthoDB protein sets for gene prediction experiments |
last update 2024-09-08formatting: failedlinting: failed |
7 |
2 |
||
No description available. |
last update 2024-07-23formatting: failedlinting: failed |
7 |
1 |
||
Snakemake pipeline for Popoolation and Popoolation2 |
ngs population genomics popoolation popoolation2 bowtie2 samtools snakemake snakemake-workflows workflow |
last update 2024-05-17formatting: passedlinting: passed |
7 |
4 |
|
snakemake workflow for performing a global sensitivity analysis of an OSeMOSYS model |
global-sensitivity-analysis gsa osemosys sensitivity-analysis |
last update 2024-04-25formatting: failedlinting: failed |
7 |
1 |
|
No description available. |
last update 2024-04-17formatting: failedlinting: failed |
7 |
2 |
||
Cell cycle analysis of single-cell proteomic and transcriptomic data for the FUCCI cell model – RNA… |
last update 2023-03-20formatting: failedlinting: failed |
7 |
3 |
||
A Snakemake workflow for Fermi-LAT data reduction |
data-reduction fermi-lat fermitools gammapy snakemake |
last update 2023-10-20formatting: failedlinting: failed |
7 |
1 |
|
Software package for the estimation of rooftop photovoltaic potential with satellite imagery |
last update 2023-05-22formatting: failedlinting: failed |
7 |
1 |
||
No description available. |
last update 2023-04-14formatting: failedlinting: failed |
7 |
4 |
||
A single-cell RNA-seq pipeline |
last update 2023-06-18formatting: failedlinting: failed |
7 |
1 |
||
Snakemake workflow for comparison of differential abundance ranks |
bioinformatics workflow differential-abundance machine-learning metagenomics microbiome pipeline snakemake |
last update 2022-08-14formatting: passedlinting: passed |
7 |
1 |
|
Novel insertion detection with 10X reads |
last update 2022-08-06formatting: failedlinting: failed |
7 |
3 |
||
No description available. |
last update 2022-11-30formatting: failedlinting: failed |
7 |
1 |
||
Snakemake workflow to benchmark scRNA-seq data simulators |
scrna-seq simulation benchmark snakemake |
last update 2022-08-10formatting: failedlinting: failed |
7 |
2 |
|
A pipeline for Bacterial Whole genome sequence data analysis |
tuberculosis workflow pipeline tb wgs |
last update 2022-07-19formatting: failedlinting: failed |
7 |
1 |
|
GIAB pipeline for benchmarking genome assemblies |
last update 2022-06-13formatting: failedlinting: failed |
7 |
2 |
||
Structural variant filtering and anlaysis of Nanopore human WGS data. |
last update 2022-10-01formatting: failedlinting: failed |
7 |
1 |
||
No description available. |
last update 2021-10-19formatting: failedlinting: failed |
7 |
2 |
||
An adaptable Snakemake workflow which uses GATKs best practice recommendations to perform germline m… |
bioinformatics-pipeline snakemake gatk4 gatk-bestpractices |
last update 2021-12-29formatting: failedlinting: failed |
7 |
1 |
|
Snakemake pipeline for amplicon sequencing using dada2 |
last update 2021-10-20formatting: failedlinting: failed |
7 |
2 |
||
VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequenc… |
last update 2022-01-20formatting: failedlinting: failed |
7 |
1 |
||
RNA-seq workflow for Snakemake based on STAR and featureCounts. |
last update 2020-12-21formatting: failedlinting: failed |
7 |
1 |
||
Pipeline for the analysis of PE ChIP-seq data |
chip-seq-pipelines snakemake |
last update 2020-12-08formatting: failedlinting: failed |
7 |
2 |
|
No description available. |
last update 2021-04-15formatting: failedlinting: failed |
7 |
2 |
||
A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(… |
last update 2020-10-27formatting: failedlinting: failed |
7 |
2 |
||
JAMIRA is a reproducible Workflow for Integrative Exploration of Genomic Features of prokariotes |
genomic-islands prophages virulence-genes resistome comparative-genomics genomic-data-analysis bioinformatics-workflow snakemake |
last update 2020-11-10formatting: failedlinting: failed |
7 |
2 |
|
No description available. |
last update 2020-04-29formatting: failedlinting: failed |
7 |
10 |
||
A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing |
last update 2021-04-23formatting: failedlinting: failed |
7 |
0 |
||
Multi-omics pipeline for the GLAMR database |
noaa-omics-software |
last update 2025-02-28formatting: failedlinting: failed |
6 |
5 |
|
Snakemake workflow for the preprocessing, alignment, QC, and quantification of spatial transcriptomi… |
last update 2025-02-28formatting: failedlinting: failed |
6 |
2 |
||
Workflow to generate interactive feature selection report for cross-sectional or longitudinal studie… |
classification exploratory-data-analysis feature-selection hypothesis-generation importance machine-learning microbiome random-forest regression |
last update 2025-02-19formatting: failedlinting: failed |
6 |
2 |
|
Guidelines for running TOGA and scripts for processing outputs |
last update 2025-02-20formatting: failedlinting: failed |
6 |
4 |
||
Workflow to identify the centromere dip regions (CDR) from methyl BAMs |
last update 2025-02-13formatting: failedlinting: failed |
6 |
1 |
||
No description available. |
last update 2025-02-13formatting: failedlinting: failed |
6 |
1 |
||
The Loaders for GraphKB. Imports content from external sources via the GraphKB REST API |
pori etl |
last update 2025-01-29formatting: failedlinting: failed |
6 |
6 |
|
An experiment to determine the relationship between spatial frequency and eccentricity in the human … |
last update 2024-09-19formatting: failedlinting: failed |
6 |
2 |
||
Bisulphite-sequencing based methylation pipeline |
last update 2024-08-13formatting: failedlinting: failed |
6 |
2 |
||
Codes to reproduce the paper How unprecedented was the February 2021 Texas cold snap? by James Doss-… |
last update 2023-01-10formatting: failedlinting: failed |
6 |
2 |
||
scRNA workflow of Cellsnake |
last update 2024-04-30formatting: failedlinting: failed |
6 |
1 |
||
An awesome Oxford Nanopore Pipeline for direct RNA-sequencing |
direct-rna-sequencing oxford-nanopore rna-editing rna-modifications singularity snakemake-pipeline bioinformatics novel-transcripts pipeline quality-control transcriptomics known-transcripts polya-tail-length-estimation alternative-splicing-analysis differential-expression-analysis |
last update 2024-04-09formatting: failedlinting: failed |
6 |
1 |
|
Pipeline to assemble oxford nanopore long sequencing reads and perform variant calling with long and… |
bioinformatics genomics nanopore nanopore-analysis-pipeline snakemake nanopore-assembly variant-calling |
last update 2024-03-24formatting: failedlinting: failed |
6 |
1 |
|
No description available. |
last update 2023-09-11formatting: failedlinting: failed |
6 |
3 |
||
No description available. |
last update 2022-12-16formatting: failedlinting: failed |
6 |
2 |
||
No description available. |
last update 2023-07-04formatting: failedlinting: failed |
6 |
2 |
||
Thirty-Two Years of IEEE VIS |
last update 2023-06-09formatting: failedlinting: failed |
6 |
2 |
||
No description available. |
last update 2023-04-19formatting: failedlinting: failed |
6 |
1 |
||
Snakemake workflow for somatic mutation detection without matched normal samples |
workflow snakemake somatic-mutations |
last update 2023-05-17formatting: failedlinting: failed |
6 |
1 |
|
Hi-C spectral analysis workflow |
last update 2022-12-13formatting: failedlinting: failed |
6 |
1 |
||
STR Detection and Counting Pipelines |
last update 2022-02-25formatting: failedlinting: failed |
6 |
2 |
||
A workflow for analysis and resistance profiling of Mycobacterium tuberculosis nanopore data with My… |
tuberculosis nanopore bioinformatics antimicrobial-resistance-genes bioinformatics-pipeline |
last update 2022-08-29formatting: failedlinting: passed |
6 |
4 |
|
Benchmarking variant calling in polyploids |
last update 2021-12-10formatting: failedlinting: failed |
6 |
4 |
||
No description available. |
last update 2021-09-20formatting: failedlinting: failed |
6 |
5 |
||
cluster stability measurement by subsampling and reclustering with Seurat V3 and V4 |
last update 2021-07-09formatting: failedlinting: failed |
6 |
2 |
||
No description available. |
last update 2021-04-15formatting: failedlinting: failed |
6 |
2 |
||
Pipeline for metagenomic community analysis using DNA isolated from virus-like particles |
last update 2021-02-18formatting: failedlinting: failed |
6 |
1 |
||
An example engineering analysis workflow for reproducible results. |
last update 2019-09-19formatting: failedlinting: failed |
6 |
1 |
||
Automated analysis and result reporting for targeted sequencing data |
last update 2020-10-15formatting: failedlinting: failed |
6 |
2 |
||
Accompanying analysis code for the FRASER manuscript |
rna-seq outlier-detection rare-disease r snakemake workflow |
last update 2021-03-22formatting: failedlinting: failed |
6 |
2 |
|
Pipeline for the processing of 3’ end sequencing libraries |
last update 2021-02-02formatting: failedlinting: failed |
6 |
1 |
||
An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq |
annotation atac-seq cell-free-dna chip-seq differential-accessibility peak-calling quality-control differential-binding bulk |
last update 2025-03-07formatting: failedlinting: failed |
5 |
5 |
|
A Snakemake pipeline for variant calling of genomic FASTQ data using GATK |
bioinformatics-workflow bioinformatics variant-calling snakemake-workflow |
last update 2025-02-25formatting: failedlinting: failed |
5 |
1 |
|
Viral Metagenomics Assembly and Annotation Pipeline |
annotation assembly classification pipeline singularity snakemake viral-metagenomics pathogen-surveillance quality-control |
last update 2025-02-14formatting: failedlinting: failed |
5 |
2 |
|
This repository contains a Snakemake pipeline which determines the species composition of the sample… |
last update 2025-02-06formatting: failedlinting: failed |
5 |
3 |
||
Plastic Enzymes Degrading in Metagenomic databases Analysis |
last update 2025-01-30formatting: failedlinting: failed |
5 |
2 |
||
Snakemake pipeline for basic processing of metagenomic data from the lab |
last update 2025-01-30formatting: failedlinting: failed |
5 |
3 |
||
Metagenomics and Metatranscriptomics pipeline |
metagenomics metatranscriptomics pipeline quality-control snakemake |
last update 2024-11-03formatting: failedlinting: failed |
5 |
2 |
|
Decoding the functional networks of non-model organisms |
last update 2024-11-12formatting: failedlinting: failed |
5 |
1 |
||
Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-… |
last update 2024-11-20formatting: failedlinting: failed |
5 |
7 |
||
Snakemake workflow to perform machine learning classification of microbiome sequence data |
last update 2024-11-16formatting: failedlinting: failed |
5 |
1 |
||
No description available. |
last update 2024-12-12formatting: failedlinting: failed |
5 |
1 |
||
Knowledge Graph generator for WorkflowHub |
last update 2024-09-24formatting: failedlinting: failed |
5 |
9 |
||
gNOMO2 allows integrated multi-omics analyses of microbiomes |
amplicon-sequencing metagenomics metaproteomics metatranscriptomics microbiome multi-omics |
last update 2024-08-07formatting: failedlinting: failed |
5 |
2 |
|
Code and data for reproducing results in the paper on identifying weather-induced power systems stre… |
last update 2024-07-29formatting: failedlinting: failed |
5 |
2 |
||
Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated… |
snakemake workflow variant-calling strelka2 gatk4-haplotypecaller deepvariant |
last update 2024-05-01formatting: failedlinting: failed |
5 |
6 |
|
Generate and combine genome assembly stats and taxonomy info. Internally used with GeneLab. |
last update 2024-02-29formatting: failedlinting: failed |
5 |
2 |
||
Example notebooks for TACCO |
last update 2024-01-05formatting: failedlinting: failed |
5 |
2 |
||
Pipeline to calculate PRS from summary statistics |
last update 2024-02-27formatting: failedlinting: failed |
5 |
9 |
||
Snakemake pipeline for quantification of deep mutational scanning (DMS) data from overlapping paired… |
last update 2023-12-15formatting: passedlinting: failed |
5 |
3 |
||
demo workflow to detect mobile genetic elements in metagenomes |
last update 2023-11-23formatting: failedlinting: failed |
5 |
1 |
||
RNA-seq pipeline for AML diagnostics developed in collaboration with the LUMC Hematology department |
last update 2022-12-14formatting: passedlinting: failed |
5 |
3 |
||
Pipeline to pull microbial reads from WGS data and perform metagenomic analysis |
bioinformatics metagenomics pipeline |
last update 2023-05-08formatting: failedlinting: failed |
5 |
4 |
|
Improving pathogenicity prediction of missense variants by using AlphaFold-derived features |
last update 2023-03-09formatting: failedlinting: failed |
5 |
3 |
||
Physics-constrained deep learning postprocessing of temperature and humidity |
last update 2023-04-04formatting: failedlinting: failed |
5 |
2 |
||
An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH |
last update 2023-03-10formatting: failedlinting: failed |
5 |
6 |
||
Scripts and results for estimating the dates of integrated HIV viruses using RNA samples from the sa… |
last update 2022-11-17formatting: failedlinting: failed |
5 |
6 |
||
A snakemake workflow for cell-free MeDIP-seq data |
last update 2022-11-01formatting: failedlinting: failed |
5 |
2 |
||
A Snakemake workflow to process paired-end RNA-Seq data. |
rna-seq snakemake |
last update 2021-09-23formatting: failedlinting: failed |
5 |
1 |
|
GWAS Summary Statistics Data Harmonisation |
last update 2022-04-07formatting: failedlinting: failed |
5 |
5 |
||
Updated version of PAQR, which was previously available in the PAQR_KAPAC joint repository. |
bioinformatics snakemake rna-seq-pipeline polyadenylation |
last update 2022-05-05formatting: failedlinting: failed |
5 |
4 |
|
Snakemake worflow to process and filter long read data from Oxford Nanopore Technologies. |
last update 2022-05-13formatting: failedlinting: failed |
5 |
1 |
||
Brief tutorial for using Snakemake to create and submit jobs on a HPC cluster. |
last update 2022-04-28formatting: failedlinting: failed |
5 |
2 |
||
A target captured medical exome ONT sequencing with amplicon variant calling workflow |
last update 2022-03-15formatting: failedlinting: failed |
5 |
5 |
||
Characterizing the neurogenomics of parental care in the rock dove |
last update 2021-12-29formatting: failedlinting: failed |
5 |
4 |
||
A de novo prediction tool of chromatin accessible regions for plant genomes |
deep-learning plant chromatin-accessibiity de-novo-prediction cnn-model open-chromatin-regions |
last update 2021-08-12formatting: failedlinting: failed |
5 |
2 |
|
A complete Snakemake pipeline for detecting allele specific expression |
snakemake allele-specific-expression rna-seq atac-seq whole-genome-sequencing |
last update 2021-07-10formatting: failedlinting: failed |
5 |
2 |
|
PEDIA-workflow prioritizes the disease-causing gene by integrating facial analysis and exome sequenc… |
last update 2020-09-23formatting: failedlinting: failed |
5 |
3 |
||
Data analysis related to the bioconda paper |
snakemake reproducibility bioconda analysis-workflows |
last update 2021-04-21formatting: failedlinting: failed |
5 |
16 |
|
A showcase and characterisation of pipeline frameworks (aka workflow managers) |
workflow-management pipeline-framework workflow-engine rosettacode |
last update 2020-12-31formatting: failedlinting: failed |
5 |
1 |
|
Benchmarking of CNV calling tools |
last update 2020-12-04formatting: failedlinting: failed |
5 |
4 |
||
Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes |
last update 2020-11-17formatting: failedlinting: failed |
5 |
1 |
||
:cake: Per sequence functional classification and taxonomic assignments |
metagenomics metatranscriptomics |
last update 2020-10-14formatting: failedlinting: failed |
5 |
2 |
|
Assembly & QA pipeline for HiFi assemblies |
last update 2025-03-07formatting: failedlinting: failed |
4 |
2 |
||
Pipeline to process sequencing reads from a ChIP-DIP experiment |
last update 2025-02-28formatting: failedlinting: failed |
4 |
6 |
||
Cut And Run Analysis Pipeline |
pipeline workflow |
last update 2025-02-27formatting: failedlinting: failed |
4 |
4 |
|
No description available. |
last update 2025-02-27formatting: failedlinting: failed |
4 |
5 |
||
No description available. |
last update 2025-02-19formatting: failedlinting: failed |
4 |
4 |
||
Snakemake workflow for (pre-)processing sci-RNA-seq3 data |
last update 2025-02-10formatting: failedlinting: failed |
4 |
3 |
||
Snakemake workflow for SINGER (ARG sampling) |
last update 2025-01-27formatting: failedlinting: failed |
4 |
2 |
||
A streamlined Oxford Nanopore Viral Metagenomics Pipeline |
pipeline snakemake annotation slim assembly singularity classification pathogen-surveillance viral-metagenomics |
last update 2025-01-29formatting: failedlinting: failed |
4 |
1 |
|
A Snakemake-based pipeline for analyzing DMS data, as used with Rosace |
last update 2025-01-21formatting: failedlinting: failed |
4 |
1 |
||
A comprehensive quality-control and quantification RNA-seq pipeline |
last update 2025-01-21formatting: failedlinting: failed |
4 |
3 |
||
Snakemake pipeline for running Virushunter and Virusgatherer |
last update 2025-01-13formatting: failedlinting: failed |
4 |
1 |
||
Workflow to annotate SNVs, indels, and structural variants |
last update 2025-01-11formatting: failedlinting: failed |
4 |
1 |
||
Workflow for functional annotation of a set of bacterial genomes |
last update 2024-11-05formatting: failedlinting: failed |
4 |
1 |
||
Workflow to analyze the genetics of drug response phenotypes derived from EHRs |
last update 2024-11-01formatting: failedlinting: failed |
4 |
1 |
||
No description available. |
last update 2024-10-31formatting: failedlinting: failed |
4 |
2 |
||
No description available. |
last update 2024-11-09formatting: failedlinting: failed |
4 |
3 |
||
No description available. |
biovis dataviz gehlenborglab python visualization gosling jupyter-notebook |
last update 2024-11-20formatting: failedlinting: failed |
4 |
1 |
|
A model of the Illinois electricity system built with PyPSA. |
last update 2024-11-23formatting: failedlinting: failed |
4 |
1 |
||
Snakemake pipeline for scATAC metacell utilities such as primed and lineage specific scores, chromVA… |
last update 2024-12-06formatting: failedlinting: failed |
4 |
1 |
||
calculate genetic diversity within multiple species using both k-mer based and snp-based approaches |
last update 2024-12-12formatting: failedlinting: failed |
4 |
1 |
||
Arcadia-Science/2024-Ecoli-amr-genotype-phenotype_7000strains |
No description available. |
last update 2024-09-17formatting: passedlinting: failed |
4 |
2 |
|
A snakemake workflow based on the obitools suite of programs, that analyzes DNA metabarcoding data. |
edna metabarcoding bioinformatics-pipeline edna-pipeline |
last update 2024-09-08formatting: failedlinting: failed |
4 |
2 |
|
MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended … |
metagenomic-analysis metagenomic-pipeline metagenomics snakemake snakemake-pipeline |
last update 2024-08-28formatting: failedlinting: failed |
4 |
1 |
|
pipeline for generating official genome-in-a-bottle stratifications |
last update 2024-05-09formatting: passedlinting: failed |
4 |
2 |
||
No description available. |
last update 2023-12-13formatting: failedlinting: failed |
4 |
0 |
||
Multiple sequence alignment pipeline |
last update 2023-12-09formatting: failedlinting: failed |
4 |
1 |
||
Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolu… |
prediction influenza modeling |
last update 2023-11-07formatting: failedlinting: failed |
4 |
17 |
|
SKA data challenge SDC2 solution |
last update 2023-05-08formatting: failedlinting: failed |
4 |
2 |
||
No description available. |
last update 2024-03-07formatting: failedlinting: failed |
4 |
5 |
||
Workflow for study hourly vs annually matched electrolytic hydrogen supply |
last update 2023-04-04formatting: failedlinting: failed |
4 |
2 |
||
No description available. |
last update 2024-03-01formatting: failedlinting: failed |
4 |
2 |
||
Snakemake pipeline for visualizing AlphaMissense pathogenicity score by UniProtID. Analysis of Aspar… |
alphamissense protein-structure |
last update 2023-11-21formatting: failedlinting: failed |
4 |
1 |
|
Ribo-DT is a snakemake pipeline to infer single-codon and codon-pair dwell times as well as gene flu… |
bioinformatics ribosome-profiling ribosome generalized-linear-models |
last update 2023-12-11formatting: failedlinting: failed |
4 |
2 |
|
No description available. |
last update 2023-03-10formatting: failedlinting: failed |
4 |
4 |
||
analysis code for Otero et al 2020 |
last update 2023-07-12formatting: failedlinting: failed |
4 |
2 |
||
RNA Biology Pipeline to Characterize protein-RNA Interactions |
last update 2023-01-26formatting: failedlinting: failed |
4 |
1 |
||
HiFi Amplicon Workflow |
last update 2023-03-14formatting: failedlinting: failed |
4 |
3 |
||
BIDS app to facilitate determining which set of experimental confounds to include in a standard task… |
last update 2023-01-09formatting: failedlinting: failed |
4 |
2 |
||
DMS of the Omicron BA.1 and BA.2 RBDs |
last update 2023-01-02formatting: failedlinting: failed |
4 |
4 |
||
Graphical model for taxonomic profiling |
last update 2023-05-17formatting: failedlinting: failed |
4 |
1 |
||
Snakemake pipeline for single-cell long-read sequencing |
last update 2023-03-19formatting: failedlinting: failed |
4 |
1 |
||
Step-by-step instructions and Snakemake pipeline for processing Cut&Run data |
bioinformatics chromatin ngs pipeline snakemake cut-and-run |
last update 2023-02-08formatting: failedlinting: failed |
4 |
0 |
|
Code for market value paper with Lina Reichenberg |
last update 2023-04-11formatting: failedlinting: failed |
4 |
2 |
||
Simple template for running snakemake with R |
r-workflow snakemake snakemake-pipeline snakemake-workflow |
last update 2023-04-06formatting: failedlinting: failed |
4 |
1 |
|
Workflow for automated (e)CLIP analysis. From raw fastq to peak calling and motif analysis. |
bioinformatics clip rna-binding-proteins |
last update 2023-04-13formatting: failedlinting: failed |
4 |
4 |
|
No description available. |
last update 2022-10-05formatting: failedlinting: failed |
4 |
14 |
||
A SnakeMake workflow to analyse whole genome bisulfite sequencing data from allopolyploids. |
snakemake bisulfite-sequencing plants allopolyploid reproducibility automation workflow dna-methylation whole-genome-sequencing epigenetics |
last update 2023-01-30formatting: failedlinting: passed |
4 |
3 |
|
The repository contains the underlying workflow to the publication in Tracing Prices: a flow-based c… |
last update 2022-05-29formatting: failedlinting: failed |
4 |
1 |
||
A pipeline to annotate miRNAs, phased siRNAs and other types using a reference genome and experiment… |
last update 2022-01-17formatting: failedlinting: failed |
4 |
2 |
||
A Snakemake workflow to filter, annotate and prepare variant call format (VCF) data for scout using … |
vcf annotation-tool genomics bioinformatics-pipeline snakemake-pipeline |
last update 2022-08-17formatting: failedlinting: failed |
4 |
3 |
|
RBP module for bindz, a bioinformatics tool to detect regulators’ binding sites on RNA sequences. |
rna rna-binding-proteins bioinformatics-tool bioinformatics snakemake-workflows |
last update 2022-02-13formatting: failedlinting: failed |
4 |
6 |
|
http://rindti.readthedocs.io/ |
last update 2022-05-23formatting: passedlinting: failed |
4 |
3 |
||
discover-virome: identify and quantify viruses from metagenomic assemblies |
virome virome-workflow snakemake snakemake-workflow metagenomic-analysis metagenomic-classification |
last update 2021-12-05formatting: failedlinting: failed |
4 |
2 |
|
Snakemake workflow for functional analysis of metagenomic WGS read data. |
last update 2022-02-19formatting: failedlinting: failed |
4 |
2 |
||
A Snakemake and Docker based pipeline to create a Neo4j graph. |
neo4j docker snakemake python |
last update 2022-01-05formatting: failedlinting: failed |
4 |
2 |
|
Viral VDAP: a viral alignment, variant discovery, and annotation pipeline launched at the NCBI-Hacka… |
womenled-nih-2019 |
last update 2021-08-26formatting: failedlinting: failed |
4 |
8 |
|
Snakemake workflow for processing exome data. |
last update 2019-11-08formatting: failedlinting: failed |
4 |
1 |
||
No description available. |
last update 2020-07-22formatting: failedlinting: failed |
4 |
1 |
||
No description available. |
last update 2021-04-24formatting: failedlinting: failed |
4 |
1 |
||
A Snakemake pipeline for cellranger to process 10x single-cell RNAseq data |
last update 2020-03-06formatting: failedlinting: failed |
4 |
2 |
||
Transcriptome assembly via digital normalization with khmer and Trinity |
transcriptome-assembly ngs trinity khmer digital-normalization assembler transrate snakemake |
last update 2020-07-27formatting: failedlinting: failed |
4 |
3 |
|
Snakemake workflow to download and/or align reads to targets and produce useful outputs. |
last update 2020-10-05formatting: failedlinting: failed |
4 |
3 |
||
:snake::hamburger: A beginner’s guide to modular snakemake workflows. |
snakemake snakemake-workflow reproducible-research bioinformatics-pipeline |
last update 2021-01-04formatting: failedlinting: failed |
4 |
0 |
|
No description available. |
last update 2020-01-23formatting: failedlinting: failed |
4 |
1 |
||
No description available. |
last update 2019-09-27formatting: failedlinting: failed |
4 |
2 |
||
WES HLA Typing based on multiple alternative tools |
workflow immunology immunoinformatics sequencing exome genome |
last update 2021-03-20formatting: failedlinting: failed |
4 |
4 |
|
Snakemake workflow for modelling-to-generate-alternatives with PyPSA-Eur |
last update 2021-02-15formatting: failedlinting: failed |
4 |
4 |
||
This repository has snakemake scripts for salmon-deseq2 pipeline for RNAseq data analysis |
salmon-deseq2 snakemake-workflow |
last update 2020-09-15formatting: failedlinting: failed |
4 |
1 |
|
No description available. |
sc-nygc-jan2020 cshl-codeathon-2020 |
last update 2021-03-19formatting: failedlinting: failed |
4 |
8 |
|
Pipeline for RNA-seq analysis |
rna-seq ngs deseq2-analysis quantification pipeline ncbi sra |
last update 2021-05-09formatting: failedlinting: failed |
4 |
3 |
|
snakemake workflow comparing Genrich and MACS2 |
last update 2020-11-09formatting: failedlinting: failed |
4 |
0 |
||
Synthesize functional scoring enrichment results from several sources (GSEApy, ClusterProfiler, STRI… |
last update 2025-03-05formatting: failedlinting: failed |
3 |
1 |
||
No description available. |
last update 2025-03-04formatting: failedlinting: failed |
3 |
0 |
||
Workflow for processing cpg0016-jump profiles |
last update 2025-03-04formatting: failedlinting: failed |
3 |
5 |
||
Health Canada’s version of the R-ODAF pipeline, which includes additional visualization and pipelini… |
last update 2025-03-06formatting: failedlinting: failed |
3 |
2 |
||
An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH |
last update 2025-03-06formatting: failedlinting: failed |
3 |
3 |
||
Workflows and code for generating and filtering genome annotations with BRAKER |
last update 2025-03-06formatting: failedlinting: failed |
3 |
2 |
||
Snakemake pipeline used for assembling genomes in EBP-Nor |
last update 2025-03-06formatting: failedlinting: failed |
3 |
2 |
||
Performs archiving and transfer of Nanopore sequencing data |
archiving automation long-read minion nanopore promethion sequencing transfer |
last update 2025-03-10formatting: passedlinting: failed |
3 |
2 |
|
No description available. |
last update 2025-03-07formatting: passedlinting: failed |
3 |
10 |
||
ChIP-Seq processing pipeline on snakemake |
atac-seq chip-seq peak-calling pipeline quality-control snakemake visualization |
last update 2025-03-01formatting: failedlinting: failed |
3 |
10 |
|
Create metamers using models of the ventral stream and run experiments to validate them |
last update 2025-02-18formatting: failedlinting: failed |
3 |
1 |
||
No description available. |
last update 2025-02-10formatting: failedlinting: failed |
3 |
16 |
||
Snakemake module containing processing steps that should be performed during sequence alignment. |
last update 2025-02-13formatting: failedlinting: failed |
3 |
2 |
||
Variant calling workflow for mixed ploidy samples implemented in Snakemake and using GATK4 |
last update 2025-01-24formatting: failedlinting: failed |
3 |
1 |
||
No description available. |
last update 2025-01-16formatting: failedlinting: failed |
3 |
1 |
||
No description available. |
last update 2025-01-15formatting: failedlinting: failed |
3 |
1 |
||
PGC MDD Wave 3 Meta-analysis |
last update 2025-01-16formatting: failedlinting: failed |
3 |
2 |
||
iSofOrmS annoTAtoR pipeline Aucouturier, C., Soirat, N., Castéra, L. et al. Fine mapping of RNA isof… |
longread rnaseq-pipeline |
last update 2025-01-19formatting: failedlinting: failed |
3 |
1 |
|
Collection of rules used to call structural variants |
last update 2025-01-09formatting: failedlinting: failed |
3 |
4 |
||
Opinionated viral metagenomics workflow |
last update 2024-12-17formatting: failedlinting: failed |
3 |
2 |
||
Bacterial genome analysis using short and long reads. |
last update 2024-10-30formatting: failedlinting: failed |
3 |
1 |
||
A workflow for bacterial short reads assembly, QC, annotation, and more. |
last update 2024-10-30formatting: failedlinting: failed |
3 |
1 |
||
No description available. |
last update 2024-10-28formatting: failedlinting: failed |
3 |
3 |
||
No description available. |
noaa-omics-software |
last update 2024-10-24formatting: failedlinting: failed |
3 |
3 |
|
No description available. |
last update 2024-11-22formatting: failedlinting: failed |
3 |
3 |
||
Snakemake workflow for comprehensive ONT analysis |
last update 2024-11-08formatting: failedlinting: failed |
3 |
3 |
||
Analysis for Variant-EFFECTS experiments |
last update 2024-11-20formatting: failedlinting: failed |
3 |
6 |
||
Obtain unbiased SNPs after FASTQ files bacoded for UMI |
last update 2024-11-28formatting: failedlinting: failed |
3 |
2 |
||
General purpose Snakemake pipeline for PanTools v4. |
last update 2024-08-20formatting: failedlinting: failed |
3 |
1 |
||
Progress tracker of HiGHS performance in PyPSA problems |
last update 2024-08-20formatting: passedlinting: failed |
3 |
1 |
||
Introgression in admixed genomes |
last update 2024-09-10formatting: failedlinting: failed |
3 |
2 |
||
This repository contains the source code for the datasets used in the implementation of the dengue l… |
last update 2024-09-10formatting: failedlinting: failed |
3 |
0 |
||
Workflow for preprocessing cfDNA samples. |
last update 2024-09-12formatting: failedlinting: failed |
3 |
1 |
||
Barebones framework for creating new snakemake workflows. |
snakemake techdev templates |
last update 2024-07-16formatting: failedlinting: failed |
3 |
7 |
|
Materials for Tech-Talk: Workflows as part of reproducible and replicable science |
data-science nextflow reproducible-research snakemake workflow |
last update 2024-08-15formatting: failedlinting: failed |
3 |
1 |
|
No description available. |
last update 2024-09-18formatting: failedlinting: failed |
3 |
1 |
||
A BASE template for building pipeLINEs |
pipeline-template snakemake |
last update 2024-06-24formatting: failedlinting: failed |
3 |
1 |
|
Doss-Gollin Lab Climate Data Repository |
last update 2024-06-06formatting: passedlinting: failed |
3 |
1 |
||
Accompanying Repository for ‘Representing Edge Flows on Graphs via Sparse Cell Complexes’ Paper. |
last update 2024-06-27formatting: failedlinting: failed |
3 |
1 |
||
No description available. |
last update 2024-05-28formatting: failedlinting: failed |
3 |
1 |
||
Flu clade and mutation frequencies |
clades flu influenza mutations |
last update 2024-07-29formatting: failedlinting: failed |
3 |
10 |
|
No description available. |
last update 2024-06-25formatting: failedlinting: failed |
3 |
1 |
||
Scripts for plots used in manuscript |
last update 2024-05-09formatting: failedlinting: failed |
3 |
1 |
||
Snakemake wrapper around the Arima Capture Hi-C (CHiC) workflow |
bioinformatics genomics hi-c hic snakemake snakemake-workflow workflow |
last update 2024-03-13formatting: failedlinting: passed |
3 |
1 |
|
Snakemake workflow for evaluation of assemblies |
last update 2024-01-05formatting: failedlinting: passed |
3 |
37 |
||
A Snakemake workflow for a complete analysis of bacterial whole-genome sequencing data. |
last update 2024-02-04formatting: failedlinting: failed |
3 |
1 |
||
What can we infer about an orbit from just the RV jitter? |
last update 2023-02-02formatting: failedlinting: passed |
3 |
4 |
||
Snakemake Pipeline for processing BioMob WP2 partial genome sequencing data |
last update 2023-07-27formatting: failedlinting: failed |
3 |
9 |
||
No description available. |
last update 2023-09-27formatting: failedlinting: failed |
3 |
2 |
||
No description available. |
last update 2023-01-11formatting: failedlinting: failed |
3 |
1 |
||
cell-free ChIP-seq pipeline |
cell-free-dna chip-seq peak-annotation peak-calling quality-control snakemake cell-type-deconvolution |
last update 2022-11-28formatting: failedlinting: failed |
3 |
1 |
|
No description available. |
last update 2023-07-05formatting: failedlinting: failed |
3 |
12 |
||
No description available. |
last update 2023-06-06formatting: failedlinting: failed |
3 |
1 |
||
Porting and deploying the HiSea use case on C-SCALE |
last update 2023-06-20formatting: failedlinting: failed |
3 |
5 |
||
RADSeq tool with Snakemake workflow integration for analysis of RAD sequencing data. |
last update 2022-08-13formatting: failedlinting: passed |
3 |
1 |
||
Implementation of the 3D-Beacons client (local 3D model server) |
biohackeu20 python |
last update 2023-03-23formatting: failedlinting: failed |
3 |
7 |
|
No description available. |
last update 2023-06-06formatting: failedlinting: failed |
3 |
2 |
||
Snakemake based analysis pipeline to identify m6As from eCLIP data |
last update 2023-06-23formatting: failedlinting: failed |
3 |
1 |
||
snakemake pipeline from transcripts to annotated protein sequences |
last update 2023-05-04formatting: failedlinting: failed |
3 |
1 |
||
Snakemake pipeline to cluster proteomes in two steps with MMseqs2 and HHsearch. |
last update 2023-02-12formatting: failedlinting: failed |
3 |
1 |
||
Snakemake pipeline for variant calling using GATK |
gatk4 variant-calling snakemake pipeline |
last update 2023-03-02formatting: failedlinting: failed |
3 |
2 |
|
This repository contains different scripts to automate and visualize analysis performed for the Inte… |
hpo multiomics proteomics rare-disease rna-seq diagnostics outlier-detection |
last update 2023-03-28formatting: failedlinting: failed |
3 |
2 |
|
Amplicon data processing workflows for diversity analysis |
last update 2023-04-01formatting: failedlinting: failed |
3 |
1 |
||
(S)train (A)ssignment from (M)etagen(O)me (S)NP (A)nalysis. |
workflow metagenomics variant-calling allele-frequencies fastq |
last update 2022-04-13formatting: failedlinting: failed |
3 |
1 |
|
A small ncRNA workflow in Snakemake. |
last update 2022-12-07formatting: failedlinting: failed |
3 |
2 |
||
No description available. |
last update 2023-02-11formatting: failedlinting: failed |
3 |
1 |
||
Nanobody-tethered transposition followed by sequencing |
last update 2022-12-23formatting: failedlinting: failed |
3 |
2 |
||
A repository to conduct experiments with omnitig-related models for genome assembly. |
omnitigs genome-assembly |
last update 2022-08-04formatting: failedlinting: failed |
3 |
5 |
|
A snakemake workflow to process ATAC-seq data |
snakemake atac-seq |
last update 2022-11-29formatting: failedlinting: failed |
3 |
2 |
|
Germline Variant Calling Pipeline built in Snakemake |
bwa snakemake pipeline |
last update 2022-10-21formatting: failedlinting: failed |
3 |
3 |
|
No description available. |
last update 2022-07-06formatting: failedlinting: failed |
3 |
2 |
||
This package is a PRobabilistic Enhancer PredictIoN Tool PREPRINT |
last update 2022-06-28formatting: failedlinting: failed |
3 |
1 |
||
Supplementary Material for the MARM2.0 model |
last update 2022-07-18formatting: failedlinting: failed |
3 |
2 |
||
Quantifies relative isotope abundance from proteomics data |
last update 2022-01-07formatting: failedlinting: failed |
3 |
4 |
||
Pipeline for BS-Seq data based on snakemake |
wgbs snakemake bisulfite-sequencing pipeline bismark epigenetics dna-methylation em-seq conda snakemake-bisulfite |
last update 2022-04-01formatting: failedlinting: failed |
3 |
1 |
|
Phylogeography of Yersinia pestis. |
phylogeography plagues |
last update 2022-06-30formatting: failedlinting: failed |
3 |
1 |
|
A Snakemake workflow for large-scale SARS-CoV-2 analyses. |
snakemake sars-cov-2 |
last update 2022-03-23formatting: passedlinting: failed |
3 |
4 |
|
Bitextor Neural generates translation memories from multilingual websites using state-of-the-art Mac… |
last update 2021-12-14formatting: failedlinting: failed |
3 |
7 |
||
This Repository includes the project of the Biof501 Course |
last update 2022-03-21formatting: failedlinting: failed |
3 |
1 |
||
MToolBox pipeline written in snakemake to allow a better scalability |
mitochondria genomics snakemake mtoolbox |
last update 2022-02-17formatting: failedlinting: failed |
3 |
3 |
|
The repository for the Snakemake implementation of the ImcSegmentationPipeline |
last update 2021-11-16formatting: failedlinting: failed |
3 |
4 |
||
Code to reproduce analyses shown in the Signac paper |
last update 2021-12-20formatting: failedlinting: failed |
3 |
1 |
||
No description available. |
last update 2021-10-13formatting: failedlinting: failed |
3 |
6 |
||
Comparative analysis of the genomes from two Acanthamoeba castellanii strains |
last update 2022-02-17formatting: failedlinting: failed |
3 |
1 |
||
No description available. |
last update 2019-08-21formatting: failedlinting: failed |
3 |
22 |
||
Consistency pipeline for hierarchies of orthologous groups (OGs) based on subsampling and tree recon… |
last update 2020-12-22formatting: failedlinting: failed |
3 |
2 |
||
No description available. |
last update 2020-08-19formatting: failedlinting: failed |
3 |
2 |
||
Command line bioinformatics workflows, created with Snakemake workflow management tool. |
last update 2021-03-26formatting: failedlinting: failed |
3 |
11 |
||
Snakemake ProtoWorkflow for DNA Analysis. |
snakemake dna bioconda |
last update 2020-11-28formatting: failedlinting: failed |
3 |
2 |
|
Snakemake pipeline to produce figures for Measuring the distribution of fitness effects in somatic e… |
last update 2020-08-29formatting: failedlinting: failed |
3 |
1 |
||
Bulk Typing of Bacterial Species down to Strain Level |
last update 2020-07-17formatting: failedlinting: failed |
3 |
2 |
||
minimal example to demonstrate flexible targeting in snakemake |
last update 2020-04-22formatting: failedlinting: failed |
3 |
1 |
||
Snakemake workflow for processing CNV-seq data. |
last update 2021-01-30formatting: failedlinting: failed |
3 |
2 |
||
Deep learning model for predicting environmental variables on river systems |
last update 2021-04-26formatting: failedlinting: failed |
3 |
5 |
||
ESI for Coarse-grained modelling for soft matter scattering |
last update 2020-06-01formatting: failedlinting: failed |
3 |
1 |
||
Snakemake workflow to run transdecoder + trinotate |
transcriptome snakemake snakemake-workflows trinity transdecoder trinotate blast hmmscan sqlite |
last update 2021-04-16formatting: failedlinting: failed |
3 |
1 |
|
This is an human RNAseq variant calling workflow, following the GATK pipeline. Also includes ADAR-si… |
last update 2020-02-01formatting: failedlinting: failed |
3 |
1 |
||
Unified sub-grid-scale parametrization using neural networks |
last update 2020-12-06formatting: failedlinting: failed |
3 |
1 |
||
A Snakemake pipeline to analyse RNA-Seq reads |
last update 2020-09-16formatting: failedlinting: failed |
3 |
3 |
||
single-cell sequencing of flu infected cells enriched for IFN+ ones |
last update 2020-11-23formatting: failedlinting: failed |
3 |
2 |
||
Pipeline for reproduction of NealeLab 2018 UKB GWAS |
last update 2021-01-21formatting: failedlinting: failed |
3 |
3 |
||
No description available. |
last update 2021-04-06formatting: failedlinting: failed |
3 |
0 |
||
Mutational antigenic profiling of Crowe-lab antibodies to SARS-CoV-2 RBD |
last update 2021-03-27formatting: failedlinting: failed |
3 |
1 |
||
Pipeline to annotate peptide identifications when using protein databases made by of ProHap / ProVar |
last update 2025-03-05formatting: failedlinting: failed |
2 |
2 |
||
No description available. |
last update 2025-03-03formatting: failedlinting: failed |
2 |
3 |
||
No description available. |
last update 2025-03-03formatting: passedlinting: failed |
2 |
1 |
||
A snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of ribosomal gene… |
last update 2025-03-06formatting: failedlinting: failed |
2 |
2 |
||
Estimación de turbidez en el agua a la entrada de la planta de tratamiento de SAMEEP, utilizando los… |
github-actions modeling python r random-forest sentinel-2 snakemake turbidity water water-quality calidad-agua gistaq s2-msi turbidez |
last update 2025-03-09formatting: failedlinting: failed |
2 |
1 |
|
A Snakemake workflow for high-throughput AlphaFold 3 structure predictions |
last update 2025-03-07formatting: failedlinting: failed |
2 |
1 |
||
This repository streamlines the extraction of time series from American Community Survey 5-Year Data… |
last update 2025-02-28formatting: passedlinting: failed |
2 |
4 |
||
No description available. |
last update 2025-02-27formatting: failedlinting: failed |
2 |
2 |
||
No description available. |
bioinformatics cancer-genomics immunology neoepitopes transcriptomics |
last update 2025-02-26formatting: failedlinting: failed |
2 |
3 |
|
Collection of rules performing QC and generating reports. |
last update 2025-02-26formatting: failedlinting: failed |
2 |
4 |
||
Public version of bksnake - biokit snakemake - bulk RNASeq Snakemake workflow |
last update 2025-02-28formatting: failedlinting: failed |
2 |
2 |
||
No description available. |
last update 2025-02-28formatting: failedlinting: failed |
2 |
1 |
||
A Snakemake workflow to find SARS-CoV-2 clusters in a reference phylogeny and estimate their normali… |
bioinformatics sars-cov-2 snakemake transmission |
last update 2025-02-18formatting: failedlinting: failed |
2 |
0 |
|
No description available. |
last update 2025-02-17formatting: failedlinting: failed |
2 |
2 |
||
Code repository accompanying the manuscript, Symbiont loss and gain, rather than co-diversification … |
last update 2025-02-21formatting: failedlinting: failed |
2 |
2 |
||
🦠 SporeFlow: ITS and 16S metataxonomics pipeline |
fungi its pipeline qiime2 snakemake workflow metataxonomics 16s |
last update 2025-02-11formatting: failedlinting: failed |
2 |
2 |
|
HBV Nanopore |
last update 2025-02-13formatting: failedlinting: failed |
2 |
5 |
||
Pipeline to predict miRNAs from host affecting metagenome sequences |
last update 2025-02-14formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2025-02-03formatting: failedlinting: failed |
2 |
1 |
||
A pipeline for Oxford Nanopore Technologies single-cell transcriptomics (10x) |
last update 2025-02-06formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2025-02-06formatting: failedlinting: failed |
2 |
3 |
||
No description available. |
last update 2025-01-27formatting: failedlinting: failed |
2 |
2 |
||
NIRISS Pure Parallel Processing Scripts |
last update 2025-01-27formatting: failedlinting: failed |
2 |
4 |
||
VirMake is a Snakemake based pipeline that offers viral metagenic data analysis on paired-end data. … |
last update 2025-01-27formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2025-01-29formatting: failedlinting: failed |
2 |
1 |
||
LEGEND data flow management |
data-processing legend snakemake |
last update 2025-02-02formatting: failedlinting: failed |
2 |
6 |
|
Price Formation in 100% Variable Renewable Energy Systems |
last update 2025-01-31formatting: passedlinting: failed |
2 |
4 |
||
No description available. |
last update 2025-01-21formatting: failedlinting: failed |
2 |
3 |
||
Single-Cell RNA-seq analysis workflow for 10x Genomics data |
bioinformatics sc-rna-seq seurat 10xgenomics snakemake differential-expression |
last update 2025-01-20formatting: failedlinting: failed |
2 |
1 |
|
A containerized implementation of the VAMBN approach by TA6.4. |
data-generation differential-privacy synthetic-data |
last update 2025-01-09formatting: passedlinting: failed |
2 |
4 |
|
Collection of rules used to create references, panel of normals (PoN), and background filters. |
last update 2025-01-09formatting: failedlinting: failed |
2 |
4 |
||
A snakemake pipeline to call structure variants from ONT data |
long-read-sequencing oxford-nanopore-sequencing structural-variants structural-variation-calling bioinformatics bioinformatics-pipeline structural-variations |
last update 2024-12-15formatting: failedlinting: failed |
2 |
2 |
|
Amplicon sequencing workflow with snakemake and dada2 |
dada2 snakemake 16s-rrna 16srrna |
last update 2024-12-14formatting: failedlinting: failed |
2 |
1 |
|
Circrnas in Host And viRuses anaLysis pIpEline for Detection Annotation Quantification of circRNAs |
circrna circularrna-detection ngs-analysis ngs-pipeline |
last update 2024-12-16formatting: failedlinting: failed |
2 |
3 |
|
id putatively mobile genomic regions |
last update 2024-12-18formatting: failedlinting: failed |
2 |
2 |
||
Pipeline for analyzing deep mutational scanning (DMS) of viral entry proteins (VEPs) |
last update 2024-12-20formatting: passedlinting: failed |
2 |
6 |
||
RNA-Seq pipeline for bulk, paired-end data |
last update 2024-12-18formatting: failedlinting: failed |
2 |
3 |
||
A workflow for genomic analysis of bacterial long reads. |
last update 2024-10-30formatting: failedlinting: failed |
2 |
1 |
||
REANA example - CMS Higgs-to-four-leptons analysis |
last update 2024-10-29formatting: failedlinting: failed |
2 |
18 |
||
Example project repository to showcase my blog post A Data Scientist’s Guide to a Comprehensive Setu… |
conda data-science github jupyterlab reproducibility snakem |
last update 2024-11-16formatting: failedlinting: failed |
2 |
1 |
|
No description available. |
last update 2024-10-31formatting: failedlinting: failed |
2 |
4 |
||
Bioinformatics_Learning_lab |
last update 2024-11-15formatting: failedlinting: failed |
2 |
2 |
||
Sources for sketch-based all-hits read mapping paper |
last update 2024-11-13formatting: failedlinting: failed |
2 |
3 |
||
No description available. |
last update 2024-11-09formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2024-11-20formatting: passedlinting: failed |
2 |
2 |
||
Snakemake workflow to genotype any type of NGS sample |
last update 2024-11-25formatting: failedlinting: failed |
2 |
2 |
||
Collections of rules to annotate vcf files. |
last update 2024-11-22formatting: failedlinting: failed |
2 |
3 |
||
Pipeline for building topologically-constrained phylogenies from DNA barcode data |
dna-barcoding metabarcoding phylogenetic-diversity phylogenetic-placement phylogenetics |
last update 2024-12-04formatting: failedlinting: failed |
2 |
9 |
|
No description available. |
last update 2024-12-09formatting: failedlinting: failed |
2 |
1 |
||
CLIP pipeline |
last update 2024-09-06formatting: failedlinting: failed |
2 |
5 |
||
No description available. |
noaa-omics-software |
last update 2024-08-27formatting: failedlinting: failed |
2 |
3 |
|
No description available. |
last update 2024-09-20formatting: failedlinting: failed |
2 |
1 |
||
energy 2050+ |
last update 2024-09-23formatting: failedlinting: failed |
2 |
2 |
||
Caprion pilot study |
proteomics gwas |
last update 2024-09-21formatting: failedlinting: failed |
2 |
3 |
|
Warlock is a snakemake workflow to spawn multiple demons (deme-based oncology models) as jobs runnin… |
mathematical-modelling oncology simulations applied-mathematics snakemake snakemake-workflow tumor tumor-evolution |
last update 2024-07-22formatting: failedlinting: failed |
2 |
2 |
|
No description available. |
last update 2024-09-14formatting: failedlinting: failed |
2 |
0 |
||
Code for processing single-molecule footprinting data on synthetic amplicons (from Doughty*, Hinks*,… |
last update 2024-07-18formatting: failedlinting: failed |
2 |
13 |
||
No description available. |
last update 2024-07-17formatting: failedlinting: failed |
2 |
3 |
||
A Snakemake pipeline analyzes paired-end mRNA-seq data to generate raw count tables and quality cont… |
last update 2024-07-23formatting: failedlinting: failed |
2 |
2 |
||
No description available. |
last update 2024-08-01formatting: failedlinting: failed |
2 |
2 |
||
No description available. |
last update 2024-08-15formatting: failedlinting: failed |
2 |
1 |
||
Bioinformatics pipeline for analyzing metagenomic data |
last update 2024-06-27formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2024-06-25formatting: failedlinting: failed |
2 |
2 |
||
No description available. |
last update 2024-06-24formatting: failedlinting: failed |
2 |
2 |
||
Improving the quality AlphaFold predicted protein complex structure by MSA optimization |
last update 2024-06-21formatting: failedlinting: failed |
2 |
2 |
||
Cross validation workflow of TensorLy |
last update 2024-06-11formatting: failedlinting: failed |
2 |
1 |
||
Code to reproduce key analyses in GWAS of heart failure subtypes and DCM from the HERMES Consortium |
last update 2024-05-22formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2024-05-11formatting: failedlinting: failed |
2 |
3 |
||
A Snakemake workflow for generating expression count tables from either locally stored fastq files o… |
last update 2024-07-02formatting: failedlinting: passed |
2 |
2 |
||
Accerating pan-biobank GWAS using phenotype projections |
genetics gwas phenotypes |
last update 2024-06-23formatting: failedlinting: failed |
2 |
3 |
|
Code and data for reproducing results in the paper on European regional and continental design flexi… |
last update 2024-04-24formatting: failedlinting: failed |
2 |
2 |
||
👨💻🧬 Trends in Bioinformatics Software Development 💻📈 |
bioinformatics development github pubmed software |
last update 2024-04-10formatting: failedlinting: failed |
2 |
2 |
|
Snakemake workflow for detecting genetics variants (snp, indels, and structural variants) in cell po… |
last update 2022-10-25formatting: failedlinting: failed |
2 |
1 |
||
A snakemake workflow for assembly with HiFi |
last update 2024-05-01formatting: failedlinting: failed |
2 |
4 |
||
No description available. |
last update 2024-02-19formatting: failedlinting: failed |
2 |
3 |
||
A pipeline for TotalRNA analysis |
metatranscriptomic-pipeline metatranscriptomics snakemake-workflow |
last update 2024-05-27formatting: passedlinting: passed |
2 |
1 |
|
De novo Long-read Genome Assembly Pipeline |
last update 2024-03-07formatting: failedlinting: failed |
2 |
2 |
||
Snakemake workflow to automatically build and organize reference genomes for common alignment tasks |
genomics rna-seq |
last update 2024-05-03formatting: failedlinting: failed |
2 |
1 |
|
No description available. |
last update 2022-09-12formatting: failedlinting: failed |
2 |
4 |
||
Exploring the panregulome of grasses with model species Brachypodium distachyon |
last update 2023-11-14formatting: failedlinting: failed |
2 |
1 |
||
A |
last update 2024-01-14formatting: failedlinting: failed |
2 |
3 |
||
population structural variant calling with smoove |
bioinformatics pipeline snakemake snakemake-pipeline structural-variation structural-variation-calling smoove vep plink survivor |
last update 2024-03-13formatting: failedlinting: failed |
2 |
1 |
|
No description available. |
last update 2024-01-25formatting: passedlinting: failed |
2 |
2 |
||
Using snakemake to run RNA-Seq |
last update 2024-01-04formatting: failedlinting: failed |
2 |
1 |
||
yetAnotherAutoTranscriptAssemblyPipeline |
last update 2022-09-17formatting: failedlinting: failed |
2 |
4 |
||
No description available. |
last update 2023-12-19formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2023-12-12formatting: failedlinting: failed |
2 |
1 |
||
Workflow for functional annotation of large collections of protein sequences |
last update 2023-12-04formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2023-09-23formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2023-07-30formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2023-12-06formatting: failedlinting: failed |
2 |
3 |
||
No description available. |
last update 2023-10-31formatting: failedlinting: failed |
2 |
2 |
||
No description available. |
last update 2023-11-06formatting: failedlinting: failed |
2 |
0 |
||
This is the epiGBS2 snakemake pipeline as published in a preprint version. |
last update 2022-11-15formatting: failedlinting: failed |
2 |
2 |
||
No description available. |
last update 2023-11-27formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2023-10-06formatting: failedlinting: failed |
2 |
1 |
||
Pipeline to build a large human reference panel, using publicly available genomes |
last update 2022-12-14formatting: passedlinting: failed |
2 |
2 |
||
Awesome single-cell CITE-sequencing Pipeline |
pipeline singularity single-cell cite-seq quality-control 10xgenomics |
last update 2022-07-19formatting: failedlinting: failed |
2 |
1 |
|
a snakemake workflow for reproducible metabarcoding |
last update 2023-04-11formatting: failedlinting: failed |
2 |
4 |
||
Produce phylogenomic trees with thousands of orthologous gene sequences from OrthoDB. Then only requ… |
bioinformatics evolution phylogenetics |
last update 2023-06-08formatting: failedlinting: failed |
2 |
2 |
|
Snakemake module for performing Mitochondrial short variant discovery |
last update 2023-01-15formatting: failedlinting: failed |
2 |
4 |
||
Improved T-cell Receptor Antigen Pairing |
last update 2023-05-05formatting: failedlinting: failed |
2 |
0 |
||
Takes raw GPS data, cleans for input into visit detection algorithm, cleans outputs and pushes data … |
last update 2023-05-05formatting: failedlinting: failed |
2 |
2 |
||
code to accompany paper ‘A Cross-Linguistic Pressure for Uniform Information Density in Word Order’ |
last update 2023-07-01formatting: failedlinting: failed |
2 |
1 |
||
Survey of ACE2 binding specificities among SARS-related CoV homologs |
last update 2022-08-04formatting: failedlinting: failed |
2 |
1 |
||
TIGER Snakemake pipeline |
last update 2022-11-02formatting: failedlinting: failed |
2 |
2 |
||
HGSVC SIG: targeted chromsome Y assembly |
last update 2023-02-15formatting: failedlinting: failed |
2 |
2 |
||
analyze substitution rate and mutation behavior within variants. |
last update 2023-02-15formatting: failedlinting: failed |
2 |
3 |
||
General rules could be used for specific purpose |
last update 2023-02-25formatting: failedlinting: failed |
2 |
1 |
||
Genomic prediction of amino acid traits in Arabidopsis seeds |
genomic-prediction amino-acids arabidopsis genomic-partitioning snakemake cookiecutter-data-science |
last update 2023-03-07formatting: failedlinting: failed |
2 |
1 |
|
Genetic architecture of Alzheimer’s disease |
last update 2023-01-25formatting: failedlinting: failed |
2 |
2 |
||
Snakemake wrapper for AHRD |
last update 2022-10-29formatting: failedlinting: failed |
2 |
1 |
||
M. tuberculosis variant identification (deprecated 2023). Use: https://github.com/ksw9/mtb-vars |
last update 2023-05-17formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2023-02-18formatting: failedlinting: failed |
2 |
2 |
||
Identify and count PacBio Hifi amplicons |
last update 2023-02-16formatting: failedlinting: failed |
2 |
1 |
||
Snakemake pipeline for detecting, annotating, filtering and visualising structure variations and ge… |
structure-variants snakemake pipeline gene fusion |
last update 2023-02-26formatting: failedlinting: failed |
2 |
2 |
|
Snakemake workflow for metagenomic analysis of rumen samples from sheep |
last update 2023-01-31formatting: failedlinting: failed |
2 |
1 |
||
Paired-end RNAseq data processing workflow designed for execution on the BigPurple HPC. Primary soft… |
pipeline rna-seq |
last update 2023-01-10formatting: failedlinting: failed |
2 |
2 |
|
Simulate short sequencing reads from coding and non-coding portions of bacterial and archaeal genome… |
last update 2023-02-11formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2023-02-07formatting: failedlinting: failed |
2 |
2 |
||
The snakemake workflow for whole-exome sequencing analysis and generating vcf files |
ngs wes snakemake-workflows |
last update 2023-01-09formatting: failedlinting: failed |
2 |
1 |
|
Design rRNA subtraction probes |
last update 2022-07-20formatting: failedlinting: failed |
2 |
1 |
||
Snakemake implementation of GATK4 pipeline for GTEx Project |
last update 2021-11-23formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2022-11-23formatting: passedlinting: failed |
2 |
2 |
||
No description available. |
last update 2022-11-21formatting: failedlinting: failed |
2 |
1 |
||
Performance analyses of classifier ensembles on peptide encodings |
last update 2022-11-21formatting: failedlinting: failed |
2 |
1 |
||
Post-processing pipeline for next-generation circulating methylome data generated by cfMeDIP-seq |
last update 2022-02-04formatting: failedlinting: failed |
2 |
2 |
||
Proyecto: Evaluación de la regulación trans en cáncer: un enfoque de biología de sistemas |
last update 2022-10-26formatting: failedlinting: failed |
2 |
4 |
||
Analysis pipeline associated with master’s thesis on the population structure, demographic history a… |
birch pipeline population-genetics |
last update 2022-09-27formatting: failedlinting: failed |
2 |
1 |
|
Anlysis of pharmacogenomic targets from Genomic Medicine Swedens heamatology panel. |
last update 2022-09-29formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2022-11-03formatting: failedlinting: failed |
2 |
2 |
||
No description available. |
last update 2022-10-06formatting: failedlinting: failed |
2 |
1 |
||
Python tools for metagenomic data |
last update 2022-08-21formatting: failedlinting: failed |
2 |
2 |
||
No description available. |
last update 2022-08-15formatting: failedlinting: failed |
2 |
2 |
||
Example code for snakemake workshop |
last update 2022-08-12formatting: failedlinting: failed |
2 |
1 |
||
Reproducibility and package management : workflow languages (CWL, Snakemake, Conda). |
last update 2022-08-03formatting: failedlinting: failed |
2 |
4 |
||
Neural Networks based unified physics parameterization for atmospheric models |
last update 2021-03-03formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2022-05-14formatting: passedlinting: failed |
2 |
1 |
||
Repository to store the analysis of the paper on phage evolution. |
last update 2022-09-08formatting: failedlinting: failed |
2 |
3 |
||
No description available. |
last update 2022-06-29formatting: failedlinting: passed |
2 |
4 |
||
The manuscript accompanying the OptiFit algorithm in mothur |
mothur snakemake microbiome reproducible-paper |
last update 2021-12-16formatting: failedlinting: failed |
2 |
3 |
|
Snakemake Workflow For WGBS Data |
last update 2022-01-10formatting: failedlinting: failed |
2 |
3 |
||
No description available. |
last update 2022-06-10formatting: failedlinting: failed |
2 |
1 |
||
demo of Papermill running on NeSI |
last update 2022-07-29formatting: failedlinting: failed |
2 |
6 |
||
A Snakemake workflow for single-cell RNA-seq analysis |
scrna-seq snakemake workflow |
last update 2022-06-22formatting: failedlinting: failed |
2 |
1 |
|
Convert NCBI assembly_summary files into sourmash taxonomy databases. |
last update 2022-04-20formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2022-07-23formatting: failedlinting: failed |
2 |
5 |
||
A Snakemake workflow for fungal metatranscriptomics |
last update 2022-02-15formatting: failedlinting: failed |
2 |
5 |
||
A snakemake workflow for performing metatranscriptomics |
last update 2022-02-16formatting: failedlinting: failed |
2 |
1 |
||
SARS-CoV-2 sequencing workflow |
snakemake-workflow snakemake workflow sars-cov-2 covid-19 covid-19-estonia korogeno-est sarscov2-variation snakefile consensus-sequences |
last update 2022-01-26formatting: failedlinting: failed |
2 |
2 |
|
No description available. |
last update 2021-10-22formatting: failedlinting: failed |
2 |
1 |
||
Interpretation of Pathogenicity of Copy Number Variants |
last update 2022-03-04formatting: failedlinting: failed |
2 |
2 |
||
Snakemake pipeline for de novo transcriptome assembly with 454 reads |
last update 2022-01-10formatting: failedlinting: failed |
2 |
2 |
||
No description available. |
last update 2022-04-12formatting: failedlinting: failed |
2 |
2 |
||
Method to detect 3’UTR changes from scRNA-seq |
scrnaseq bioinformatics snakemake-workflow |
last update 2021-12-16formatting: failedlinting: failed |
2 |
5 |
|
Automated de novo transcriptome assembly |
last update 2021-12-06formatting: failedlinting: failed |
2 |
2 |
||
A proof-of-concept, automated and reproducible pipeline for predicting functional associations betwe… |
bacteriophages machine-learning bioinformatics-pipeline function-prediction |
last update 2021-11-06formatting: failedlinting: failed |
2 |
0 |
|
Small snakemake best practice workflow |
last update 2022-02-12formatting: failedlinting: passed |
2 |
6 |
||
A Snakemake pipeline for constructing de novo*transcriptomes from the EiaD dataset |
last update 2021-10-14formatting: failedlinting: failed |
2 |
0 |
||
Code for replicating Right and left, partisanship predicts vulnerability to misinformation by Dimita… |
last update 2021-08-09formatting: failedlinting: failed |
2 |
2 |
||
No description available. |
last update 2021-08-09formatting: passedlinting: failed |
2 |
2 |
||
Trade-offs between geographic scale, cost, and infrastructure requirements for fully renewable elect… |
last update 2021-08-04formatting: failedlinting: failed |
2 |
2 |
||
Personal data redaction on images based on FHIR patient resources. |
document pseudonymization fhir snakemake-workflow |
last update 2021-07-22formatting: failedlinting: passed |
2 |
3 |
|
Radiogenomic analysis of breast cancer by linking MRI phenotypes with tumor gene expression |
last update 2021-06-09formatting: failedlinting: failed |
2 |
3 |
||
Snakemake workflow for CITE-seq analaysis with alevin-fry and seurat |
last update 2021-05-27formatting: passedlinting: failed |
2 |
1 |
||
Snakemake workflow for benchmarking taxonomy assignments |
last update 2020-01-29formatting: failedlinting: failed |
2 |
3 |
||
Snakemake pipeline optimized for usage on SLURM |
last update 2020-10-21formatting: failedlinting: failed |
2 |
1 |
||
A pipeline for extracting SSU rRNA gene from wgs data and applying them for further diversity analys… |
last update 2019-11-19formatting: failedlinting: failed |
2 |
1 |
||
Consolidation of tools in the MutPred Suite to work with VCF files |
last update 2019-08-01formatting: failedlinting: failed |
2 |
8 |
||
No description available. |
last update 2020-11-03formatting: failedlinting: failed |
2 |
1 |
||
Materials and Code for the micom manuscript. |
last update 2021-03-15formatting: failedlinting: failed |
2 |
1 |
||
Workflow for transcript expression analysis |
last update 2021-03-24formatting: failedlinting: failed |
2 |
1 |
||
Polyadenylation aware read trimming and alternative polyadenylation site analysis |
last update 2021-04-10formatting: failedlinting: failed |
2 |
4 |
||
a small exercise using Angrist & Krueger’s 1991 data in a reproducible workflow |
snakemake snakemake-workflow reproducible-research harmless-econometrics |
last update 2020-10-02formatting: failedlinting: failed |
2 |
1 |
|
Hand output of Atlas to Anvio |
last update 2020-07-01formatting: failedlinting: failed |
2 |
3 |
||
gatk4 workflow |
last update 2020-12-09formatting: failedlinting: failed |
2 |
0 |
||
Snakemake workflow for evaluating varlociraptor |
snakemake workflow reproducible-research |
last update 2021-03-07formatting: failedlinting: failed |
2 |
2 |
|
No description available. |
last update 2020-12-17formatting: failedlinting: failed |
2 |
1 |
||
Pipeline for CAGE data analysis using icetea |
cage-seq |
last update 2020-03-24formatting: failedlinting: failed |
2 |
1 |
|
A Snakemake workflow for TAP-seq data processing |
last update 2020-07-20formatting: failedlinting: failed |
2 |
1 |
||
No description available. |
last update 2021-04-13formatting: failedlinting: failed |
2 |
2 |
||
Mutational antigenic profiling of SARS-CoV-2 RBD against REGN-COV2 and LY-CoV016 |
last update 2021-02-09formatting: failedlinting: failed |
2 |
1 |
||
Quality control for mass spec proteomics |
workflow ms px |
last update 2020-09-24formatting: failedlinting: failed |
2 |
13 |
|
Fastq to bam mapping pipeline with marked duplicates, indexing, and insert size metric collection |
last update 2020-12-24formatting: failedlinting: failed |
2 |
1 |
||
Using the |
bookdown rticles journal-article |
last update 2019-01-15formatting: failedlinting: failed |
2 |
1 |
|
No description available. |
last update 2021-02-23formatting: failedlinting: failed |
2 |
3 |
||
Tools and workflows for evaluating bacterial and archaeal genome contamination with sourmash and GTD… |
sourmash |
last update 2021-03-05formatting: failedlinting: failed |
2 |
6 |
|
Explore car crash prediction using NZTA Crash Analysis System data |
crash-prediction nzta cas road traffic safety |
last update 2021-04-07formatting: failedlinting: failed |
2 |
1 |
|
Proteome Annotation Transfer Tool |
last update 2025-03-05formatting: failedlinting: failed |
1 |
1 |
||
Pipeline for conveniently running PRScs |
last update 2025-03-05formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2025-03-05formatting: failedlinting: failed |
1 |
1 |
||
A snakemake workflow that calls variants from multi-sample illumina reads using Deepvariant and GLne… |
last update 2025-03-07formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2025-03-06formatting: failedlinting: failed |
1 |
1 |
||
Snakemake workflow for assembling transcript models from RNA-seq reads |
last update 2025-03-06formatting: failedlinting: failed |
1 |
2 |
||
No description available. |
last update 2025-03-06formatting: failedlinting: failed |
1 |
1 |
||
Compute a sequence and structure based phylome based on uniprot proteomes. |
last update 2025-03-06formatting: failedlinting: failed |
1 |
3 |
||
Repository that contains notebooks for network validation |
last update 2025-03-06formatting: failedlinting: failed |
1 |
0 |
||
Post Sqanti QC ANalysis of long-read RNA sequencing |
last update 2025-03-05formatting: passedlinting: failed |
1 |
1 |
||
No description available. |
last update 2025-03-05formatting: failedlinting: failed |
1 |
0 |
||
No description available. |
last update 2025-03-05formatting: failedlinting: failed |
1 |
2 |
||
A snakemake pipeline for analyzing proteins, its domains, and taxonomy. |
last update 2025-03-10formatting: passedlinting: failed |
1 |
1 |
||
No description available. |
last update 2025-03-09formatting: failedlinting: failed |
1 |
0 |
||
Extensible pipeline tool for processing optical pooled screens data. |
last update 2025-03-08formatting: failedlinting: failed |
1 |
0 |
||
Snakemake pipeline to process nanopore aa-tRNA-seq data |
nanopore-sequencing rna-seq snakemake |
last update 2025-03-08formatting: passedlinting: failed |
1 |
1 |
|
Assorted short read WGS post-alignment tooling |
last update 2025-03-07formatting: failedlinting: failed |
1 |
1 |
||
Snakemake pipeline for de-novo genome assembly of PacBio HiFi reads using HiFiasm. Includes automate… |
last update 2025-03-07formatting: failedlinting: failed |
1 |
1 |
||
Short read WGS calling for PMGRC/GREGoR |
last update 2025-02-25formatting: failedlinting: failed |
1 |
1 |
||
16S amplicon processing workflow using Snakemake |
last update 2025-02-25formatting: failedlinting: failed |
1 |
1 |
||
Package for the species specific analysis WP6 MicrobeSeq |
last update 2025-02-24formatting: failedlinting: failed |
1 |
2 |
||
No description available. |
last update 2025-02-27formatting: passedlinting: failed |
1 |
2 |
||
Sparse factorization framework to integrate GWAS studies and identify shared latent genetic componen… |
factor-analysis genomics genomics-analysis statistics unsupervised-machine-learning |
last update 2025-02-27formatting: failedlinting: failed |
1 |
4 |
|
Transcript data builds for mehari |
last update 2025-02-27formatting: passedlinting: passed |
1 |
4 |
||
Significant improvement and extension of bam2bakR |
rna-seq slam-seq snakemake tuc-seq nr-seq timelapse-seq |
last update 2025-02-26formatting: passedlinting: passed |
1 |
1 |
|
Shotgun metagenomic sequencing processing pipeline |
last update 2025-02-26formatting: failedlinting: failed |
1 |
5 |
||
Bioinformatics pipeline for analyzing 16S amplicon data |
last update 2025-03-01formatting: failedlinting: failed |
1 |
3 |
||
Computing cross-species evolutionary features of orthologous genes. |
last update 2025-02-28formatting: failedlinting: failed |
1 |
1 |
||
Bioinformatics pipeline for profiling anti-microbial resistance genes from hospital wastewater |
last update 2025-02-18formatting: failedlinting: failed |
1 |
1 |
||
One single-cell pipeline to rule them all, one pipeline to find them, one pipeline to unify them all… |
single-cell-atac-seq single-cell-omics single-cell-rna-seq 10xgenomics single-cell-vdj single-cell-cite-seq |
last update 2025-02-20formatting: failedlinting: failed |
1 |
2 |
|
This is a snakemake pipeline to extract features from bacterial genomes. |
last update 2025-02-20formatting: failedlinting: failed |
1 |
3 |
||
Bioinformatics pipelines for Salmonella_Isangi genomics analysis |
last update 2025-02-20formatting: failedlinting: failed |
1 |
1 |
||
Variant Calling Snakemake Pipeline |
bioinformatics bioinformatics-pipeline variant-calling snakemake snakemake-workflow |
last update 2025-02-19formatting: passedlinting: failed |
1 |
1 |
|
No description available. |
last update 2025-02-24formatting: failedlinting: failed |
1 |
1 |
||
A beginner’s guide to snakemake |
last update 2025-02-23formatting: failedlinting: failed |
1 |
2 |
||
High throughput tool for tall and wide multiple sequence alignment. |
bioinformatics cuda multiple-sequence-alignment snakemake twilight gpu-acceleration |
last update 2025-02-21formatting: failedlinting: failed |
1 |
2 |
|
Stand-alone tool for methylation-based discrimination of mitochondrial DNA ONT reads |
bioinformatics dorado long-reads mitochondria oxford-nanopore pipeline snakemake workflow |
last update 2025-02-21formatting: failedlinting: failed |
1 |
1 |
|
No description available. |
last update 2025-02-21formatting: failedlinting: failed |
1 |
2 |
||
⚙️ 🍄 QIIME 2 TEF1 classifiers for the FUSARIUM-ID database |
last update 2025-02-11formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2025-02-11formatting: failedlinting: failed |
1 |
3 |
||
A Snakemake pipeline to prepare binary PLINK files for the Michigan Imputation Server. |
last update 2025-02-10formatting: failedlinting: failed |
1 |
1 |
||
Finding TEs with short-read data using random forests |
last update 2025-02-14formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2025-02-10formatting: failedlinting: failed |
1 |
1 |
||
Workflow for merging multi-lane fastq files from the Illumina NextSeq 550 using Snakemake. In additi… |
last update 2025-02-12formatting: failedlinting: failed |
1 |
1 |
||
Extract Finaletoolkit features from several files |
last update 2025-02-16formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2025-02-15formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2025-02-14formatting: failedlinting: failed |
1 |
1 |
||
Snakemake module for generating reports related to Hydra-Genetics results |
last update 2025-02-14formatting: failedlinting: failed |
1 |
5 |
||
No description available. |
last update 2025-02-04formatting: failedlinting: failed |
1 |
1 |
||
deep mutational scanning of the CGGnaive antibody |
last update 2025-02-03formatting: failedlinting: failed |
1 |
7 |
||
Snakemake workflow for experiments with the causalspyne Python package. |
last update 2025-02-06formatting: failedlinting: failed |
1 |
2 |
||
No description available. |
last update 2025-02-06formatting: failedlinting: failed |
1 |
1 |
||
Workflow for running the SCME code through snakemake |
last update 2025-02-08formatting: failedlinting: failed |
1 |
1 |
||
Samar is a pipeline for speedy, assembly-free differential gene expression analysis in non-model org… |
last update 2025-02-08formatting: failedlinting: failed |
1 |
1 |
||
This Snakemake workflow is designed for processing metagenomic sequencing data. |
last update 2025-02-08formatting: failedlinting: failed |
1 |
1 |
||
A collection of snakemake workflows for RNAseq, CUT-RUN, and ChIPseq analysis |
last update 2025-01-28formatting: failedlinting: failed |
1 |
1 |
||
INSinPAL : Detecting Large Insertion Events in Whole Genome Sequencing Data at Palindromic Fragile S… |
last update 2025-01-28formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2025-01-30formatting: failedlinting: failed |
1 |
1 |
||
Automated transcriptome assembly |
last update 2025-01-29formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2025-01-31formatting: failedlinting: failed |
1 |
1 |
||
Pipeline for PRS computation integrating diverse PRS algorithms into a unique Snakemake workflow. |
bioinformatics-pipeline genetics polygenic-risk-scores |
last update 2025-01-20formatting: failedlinting: failed |
1 |
3 |
|
Characterizing identification probability and precision in reference-free compound identification fo… |
last update 2025-01-14formatting: failedlinting: failed |
1 |
4 |
||
No description available. |
last update 2025-01-13formatting: failedlinting: failed |
1 |
1 |
||
Cleaning transcriptome annotations with ab initio assemblers |
last update 2025-01-16formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2025-01-16formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2025-01-16formatting: failedlinting: passed |
1 |
1 |
||
No description available. |
noaa-omics-software |
last update 2025-01-14formatting: failedlinting: failed |
1 |
2 |
|
No description available. |
last update 2025-01-17formatting: failedlinting: failed |
1 |
1 |
||
Simulation of long-read sequencing data with structural variations in human genomes |
last update 2025-01-17formatting: failedlinting: failed |
1 |
2 |
||
Collection of rules used to calculate biomarkers like MSI, TMB and HRD. |
last update 2025-01-09formatting: failedlinting: failed |
1 |
4 |
||
No description available. |
last update 2025-01-13formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-12-18formatting: failedlinting: failed |
1 |
2 |
||
Basic multi-sample variant calling workflow with GATK |
last update 2024-12-17formatting: failedlinting: failed |
1 |
2 |
||
No description available. |
last update 2024-12-17formatting: failedlinting: failed |
1 |
1 |
||
Deep mutational scanning phenotypes of clade 2.3.4.4b influenza H5 HA |
last update 2024-12-16formatting: failedlinting: failed |
1 |
2 |
||
No description available. |
last update 2024-12-18formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-10-30formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-10-29formatting: failedlinting: failed |
1 |
2 |
||
Snakemake diagnostic RNA-Seq Fusion Pipline for ALL |
last update 2024-12-09formatting: failedlinting: failed |
1 |
2 |
||
No description available. |
last update 2024-11-03formatting: failedlinting: failed |
1 |
1 |
||
Snakemake workflow to generate country-specific population density data, for use in epidemiological … |
agent-based-modeling epidemiology population-density-maps |
last update 2024-11-12formatting: failedlinting: failed |
1 |
2 |
|
Preprocess Metagenomic Data |
last update 2024-11-12formatting: passedlinting: passed |
1 |
1 |
||
No description available. |
last update 2024-11-22formatting: failedlinting: failed |
1 |
0 |
||
Short read taxonomy |
last update 2024-11-09formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-11-08formatting: failedlinting: failed |
1 |
8 |
||
Benchmark for the AI LLM integration project |
last update 2024-11-21formatting: failedlinting: failed |
1 |
46 |
||
No description available. |
last update 2024-11-21formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-12-04formatting: failedlinting: failed |
1 |
2 |
||
This pipeline uses repeatmasker, repeatmodeler, and the TREP database (https://trep-db.uzh.ch/) to … |
last update 2024-12-11formatting: failedlinting: failed |
1 |
1 |
||
Snakemake pipeline for Greenleaf lab array preprocessing. |
last update 2024-11-18formatting: failedlinting: failed |
1 |
13 |
||
No description available. |
last update 2024-11-18formatting: failedlinting: failed |
1 |
2 |
||
Typing and quantification of immune gene alleles in single cell and spatial transcriptomic data |
last update 2024-11-18formatting: failedlinting: failed |
1 |
3 |
||
No description available. |
last update 2024-11-18formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-11-28formatting: failedlinting: failed |
1 |
1 |
||
Customizeable workflow for batching multiple snakebids apps or bids apps |
last update 2024-11-27formatting: failedlinting: failed |
1 |
3 |
||
Collection of scripts for benchmarking of seq2squiggle with other nanopore sequencing simulators |
last update 2024-11-25formatting: failedlinting: failed |
1 |
1 |
||
Genome-resolved metagenomics pipeline. |
last update 2024-12-03formatting: passedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-12-02formatting: failedlinting: failed |
1 |
1 |
||
Snakemake workflow to install reference genomes and their supporting files |
last update 2024-12-01formatting: failedlinting: failed |
1 |
1 |
||
SLAV-seq analysis pipeline for SZ dataset |
last update 2024-12-01formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-12-09formatting: failedlinting: failed |
1 |
1 |
||
Snakemake DADA2-based 16S amplicon sequenicng workflow |
last update 2024-12-06formatting: failedlinting: failed |
1 |
5 |
||
No description available. |
last update 2024-12-12formatting: failedlinting: failed |
1 |
5 |
||
Project for CMSE890 Fall 2024: Reproducible Workflows. This repository is used to store a reproducib… |
last update 2024-12-11formatting: failedlinting: failed |
1 |
1 |
||
Snakemake workflow to convert illumina genotype array idats to vcf format. |
last update 2024-12-10formatting: failedlinting: failed |
1 |
1 |
||
A rapid pipeline for targeted ONT monkeypox sequencing |
conda mamba monkeypox mpox oxford-nanopore phylogenetics pipeline singularity snakemake rapid |
last update 2024-08-22formatting: failedlinting: failed |
1 |
1 |
|
No description available. |
last update 2024-08-21formatting: failedlinting: failed |
1 |
1 |
||
Repository practice project in EEAD-CSIC |
last update 2024-08-26formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-08-26formatting: failedlinting: failed |
1 |
3 |
||
No description available. |
last update 2024-09-06formatting: failedlinting: failed |
1 |
1 |
||
Random notes, scripts, et cetera |
last update 2024-09-07formatting: passedlinting: failed |
1 |
1 |
||
Customized snakemake workflow for computational image processing |
last update 2024-09-03formatting: failedlinting: failed |
1 |
2 |
||
No description available. |
last update 2024-09-02formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-09-20formatting: failedlinting: failed |
1 |
4 |
||
No description available. |
last update 2024-09-16formatting: failedlinting: failed |
1 |
4 |
||
Simple snakemake workflow for WGS variant calling |
last update 2024-09-16formatting: failedlinting: failed |
1 |
2 |
||
An experimental nanopore only 16s Amplicon analysis |
last update 2024-09-15formatting: failedlinting: failed |
1 |
1 |
||
FunFlux: A dedicated workflow for fungal genome assembly from short reads, decontamination, complete… |
last update 2024-09-20formatting: failedlinting: failed |
1 |
1 |
||
A workflow for RNA sequence alignment. |
last update 2024-09-18formatting: failedlinting: failed |
1 |
2 |
||
An awesome microRNA-sequencing pipeline |
micro-rna mirdeep2 micro-rna-expression singularity snakemake mirna mirna-seq mature-mirna |
last update 2024-09-23formatting: failedlinting: failed |
1 |
1 |
|
A snakemake pipeline for aligning UMI based WGS data and QC metrics associated with it |
last update 2024-07-23formatting: passedlinting: failed |
1 |
4 |
||
Demo repo for new cluster setup with snakemake (excludes configs) |
last update 2024-09-20formatting: passedlinting: failed |
1 |
1 |
||
A snakemake workflow for analyzing illumina WGS data of Mycobacterium Tuberculosis complex isolates |
last update 2024-08-05formatting: failedlinting: failed |
1 |
1 |
||
Repository dedicated to the experiment section of the paper: Revisiting pangenome openness with k-me… |
bacteria pangenome pangenomics |
last update 2024-08-01formatting: failedlinting: failed |
1 |
1 |
|
No description available. |
last update 2024-07-25formatting: failedlinting: failed |
1 |
0 |
||
Snakemake workflow to perform Energy Landscape Analysis |
last update 2024-08-14formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-08-12formatting: failedlinting: failed |
1 |
1 |
||
Snakemake workflow to profile MHC-I neoepitopes with bulk tumor RNAseq data |
bioinformatics cancer-genomics transcriptomics immunology neoepitopes |
last update 2024-08-12formatting: failedlinting: passed |
1 |
2 |
|
HMMER-based microcin search using full microcin sequences and double-glycine signal region. |
antimicrobial-peptides bacterial-genome-analysis bioinformatics-pipeline blast hidden-markov-model hmm hmmer hmmer3 search microcin |
last update 2024-08-27formatting: failedlinting: failed |
1 |
1 |
|
A workflow comparing different python data viz libraries |
last update 2024-09-04formatting: failedlinting: failed |
1 |
3 |
||
No description available. |
last update 2024-08-08formatting: failedlinting: failed |
1 |
1 |
||
Script for data collection |
last update 2024-08-07formatting: failedlinting: failed |
1 |
1 |
||
A quick pipeline for protein structure comparison |
last update 2024-07-16formatting: failedlinting: failed |
1 |
1 |
||
Benchmarking parabricks GPU-accelerated tools for GATK and beyond! |
last update 2024-07-19formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-08-27formatting: failedlinting: failed |
1 |
1 |
||
Building snakemake workflows with pixi ✨ |
last update 2024-07-08formatting: failedlinting: failed |
1 |
1 |
||
PCR Signature Erosion Tool |
last update 2024-06-29formatting: passedlinting: failed |
1 |
0 |
||
Snakemake workflow for validation of variant calls |
last update 2024-06-27formatting: passedlinting: failed |
1 |
1 |
||
This is the replication template for my data analysis. |
last update 2024-09-02formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-06-22formatting: failedlinting: failed |
1 |
22 |
||
Endogenous Retrovirus Expression Pipeline for Human and Mouse for use with bulk RNA |
herv human mouse quality-control endogenous-retrovirus-expression pipeline singularity snakemake workflow |
last update 2024-06-20formatting: failedlinting: failed |
1 |
2 |
|
No description available. |
last update 2024-07-02formatting: failedlinting: failed |
1 |
3 |
||
A template repository for running Virtual Rainforest analyses using Snakemake |
last update 2024-01-23formatting: passedlinting: failed |
1 |
5 |
||
Workflow to run and evaluate clustering of ASV sequences into OTUs |
last update 2024-06-10formatting: failedlinting: failed |
1 |
0 |
||
No description available. |
last update 2024-06-07formatting: failedlinting: failed |
1 |
1 |
||
HGDP Aberrations Coverage Repository |
last update 2024-05-31formatting: failedlinting: failed |
1 |
1 |
||
This is a snakemake pipeline to extract features from bacterial genomes. |
last update 2024-05-24formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-06-20formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
noaa-omics-software |
last update 2024-07-23formatting: failedlinting: failed |
1 |
2 |
|
Project template for sourmash-based characterization of genomes and metagenomes |
sourmash |
last update 2024-06-28formatting: failedlinting: failed |
1 |
3 |
|
SF Long Read Variant Analysis pipeline |
last update 2024-05-13formatting: failedlinting: failed |
1 |
2 |
||
No description available. |
last update 2024-04-29formatting: failedlinting: failed |
1 |
1 |
||
Snakemake pipeline for running automated RNAseq analysis, from fastq reads to Differential Expressio… |
last update 2024-04-29formatting: failedlinting: failed |
1 |
1 |
||
A Snakemake workflow to convert DICOM dataset to BIDS format and compute QC reports. |
last update 2024-04-29formatting: failedlinting: failed |
1 |
1 |
||
Repository for Polylox barcoding extraction scripts |
last update 2024-04-26formatting: failedlinting: failed |
1 |
2 |
||
No description available. |
last update 2024-04-25formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-05-01formatting: failedlinting: failed |
1 |
2 |
||
Using trait segmentation to understand minnow trait evolution across an ecological gradient |
last update 2024-04-22formatting: failedlinting: failed |
1 |
3 |
||
Processing pipeline for GPR68 DMS data |
last update 2024-04-19formatting: failedlinting: failed |
1 |
2 |
||
GeoHeat-GB: A geospatial power systems planning model for heat electrification in Britain |
energy energy-system energy-system-model energy-system-modeling energy-systems geospatial heat-pump heating power-systems pypsa |
last update 2024-02-06formatting: failedlinting: failed |
1 |
1 |
|
No description available. |
last update 2023-03-24formatting: failedlinting: failed |
1 |
2 |
||
Workflow to process bulk RNASeq samples using Salmon and DESeq2 |
last update 2022-04-26formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-06-13formatting: failedlinting: failed |
1 |
2 |
||
A basic template to get started with Snakemake using Pixi |
pixi snakemake |
last update 2024-04-25formatting: failedlinting: failed |
1 |
1 |
|
Snakemake pipeline to automate running multiple samples through the ENCODE ATAC-seq workflow |
last update 2022-08-01formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-01-10formatting: failedlinting: failed |
1 |
1 |
||
Parallel Annotation Pipeline |
last update 2023-04-17formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-01-27formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-04-12formatting: failedlinting: failed |
1 |
2 |
||
Performing a variant calling study using two samples of barley. For that, we used freebayes, gatk an… |
last update 2024-03-25formatting: failedlinting: failed |
1 |
1 |
||
Workflow for de novo transcriptome assemblies from paired-end illumina reads, annotation and quality… |
annotation fastq illumina transcriptomics transdecoder rna-seq-pipeline workflow-reusable python snakemake |
last update 2024-04-19formatting: failedlinting: failed |
1 |
2 |
|
This is a snakemake workflow that uses GATK4 to call SNPs against Australian Reference Z. tritici WA… |
last update 2023-04-05formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-02-20formatting: failedlinting: failed |
1 |
1 |
||
democratizing genome assembly |
last update 2022-01-20formatting: failedlinting: failed |
1 |
1 |
||
Make a nice depth plot of Strand-Seq data using my own custom composite files. |
last update 2023-11-15formatting: failedlinting: failed |
1 |
1 |
||
The PAC 2.0 project is an ambitious project aiming at exploring the implications of a PAC scenario w… |
last update 2024-02-15formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-04-25formatting: failedlinting: failed |
1 |
3 |
||
No description available. |
last update 2024-02-12formatting: failedlinting: failed |
1 |
2 |
||
Snakemake tutorial delivered at the Workshop on Basic Computing Services in the Physics Department -… |
last update 2024-02-04formatting: failedlinting: failed |
1 |
1 |
||
Snakemake module that installs gnomAD accessory files and infrastructure for maps scores |
last update 2024-01-29formatting: failedlinting: failed |
1 |
1 |
||
This repository contains code for processing of sequencing data and virus predictions, and data anal… |
last update 2024-03-10formatting: failedlinting: failed |
1 |
0 |
||
Reproduce some tables and graphs from Angrist & Krueger (1991) |
last update 2024-01-21formatting: failedlinting: failed |
1 |
1 |
||
PAPA (Pipeline-Alternative Polyadenylation) - Snakemake pipeline for analysis of APA from short-read… |
last update 2024-02-29formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2024-01-29formatting: failedlinting: failed |
1 |
1 |
||
This package contains a pipeline for prediction of RNA-RNA contacts from RIC-seq data. |
bioinformatics pipeline ric-seq |
last update 2023-11-30formatting: failedlinting: failed |
1 |
1 |
|
A pipeline for variant calling from P. falciparum short reads generated from Illumina and ONT librar… |
amplicon-sequencing illumina-sequencing malaria oxford-nanopore plasmodium-falciparum variant-calling |
last update 2023-12-19formatting: failedlinting: failed |
1 |
2 |
|
This repository contains a Snakemake workflow for the generation and visualization of virtual karyot… |
last update 2024-01-25formatting: failedlinting: failed |
1 |
4 |
||
No description available. |
last update 2023-12-18formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2023-12-15formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2023-11-20formatting: failedlinting: failed |
1 |
1 |
||
Code for Broad Ranges of Investment Configurations… |
last update 2022-12-13formatting: failedlinting: failed |
1 |
2 |
||
No description available. |
last update 2023-08-25formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2023-10-16formatting: failedlinting: failed |
1 |
1 |
||
Instructions and examples for using PanVC with founder sequences |
founder-sequences variant-calling next-generation-sequencing |
last update 2022-08-25formatting: failedlinting: failed |
1 |
6 |
|
Automated Assessment of Trait-specific Evolutionary Adaptations |
last update 2023-03-12formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2023-10-09formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2023-07-20formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2022-01-05formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2023-11-28formatting: failedlinting: failed |
1 |
2 |
||
Diffusion models for probabilistic programming |
diffusion-models jax probabilistic-models probabilistic-programming variational-inference |
last update 2023-11-07formatting: failedlinting: failed |
1 |
2 |
|
Automated Detection and Qualification of Differential Methylation |
last update 2023-11-08formatting: failedlinting: failed |
1 |
1 |
||
IS477-Fall2023 final project repository. |
last update 2023-11-30formatting: failedlinting: failed |
1 |
1 |
||
Snakemake implementation of TimeLapse pipeline developed by Simon lab |
last update 2023-03-26formatting: failedlinting: failed |
1 |
1 |
||
Example Nextstrain workflow based on public SARS-CoV-2 sequences from GenBank |
last update 2022-01-26formatting: failedlinting: passed |
1 |
1 |
||
An awesome BCL demultiplexing and FastQ quality-control pipeline |
bcl2fastq bclconvert contamination-screening disambiguate-genomes fastq-quality-control fastp kaiju kraken2 krona |
last update 2023-11-30formatting: failedlinting: failed |
1 |
2 |
|
Research project exploring multiplex reconstruction techniques informed by graph embeddings. |
graph-embeddings multiplex-networks network-analysis reconstruction-algorithm |
last update 2023-10-19formatting: failedlinting: failed |
1 |
2 |
|
VirMake is a Snakemake based pipeline that offers viral metagenic data analysis on paired-end data. … |
masterthesis |
last update 2023-07-07formatting: failedlinting: failed |
1 |
2 |
|
Extended genecatalog workflow for metagenome-atlas |
last update 2021-11-03formatting: failedlinting: failed |
1 |
2 |
||
No description available. |
last update 2023-09-27formatting: failedlinting: failed |
1 |
2 |
||
A snakemake pipeline to analyze SSR/STR data and call markers in VCF format using HipSTR (https://hi… |
last update 2023-03-05formatting: failedlinting: failed |
1 |
2 |
||
rna-seq-snakemake |
last update 2022-09-09formatting: failedlinting: failed |
1 |
1 |
||
Snakemake workflow to generate reference genomes and annotations |
last update 2023-09-14formatting: failedlinting: failed |
1 |
1 |
||
A pipeline for simulating viral or vector integration into a host genome |
last update 2022-07-15formatting: failedlinting: failed |
1 |
8 |
||
Boilerplate for Snakemake workflow |
last update 2023-09-15formatting: passedlinting: failed |
1 |
1 |
||
Endogenous Retrovirus Expression Pipeline for Human and Mouse for use with data from 10x genomics (b… |
endogenous-retrovirus-expression single-cell-rna-seq |
last update 2023-09-01formatting: failedlinting: failed |
1 |
2 |
|
No description available. |
last update 2022-12-09formatting: failedlinting: failed |
1 |
1 |
||
Snakemake project template that can be executed on the turso federation (ukk02/vorna/…) |
last update 2023-06-01formatting: failedlinting: failed |
1 |
2 |
||
Single Cell Copy Number Evolutionary Analysis |
last update 2023-06-27formatting: failedlinting: failed |
1 |
1 |
||
Worklflow managers are good mkay |
last update 2023-06-27formatting: failedlinting: passed |
1 |
8 |
||
No description available. |
last update 2023-04-14formatting: passedlinting: failed |
1 |
2 |
||
No description available. |
last update 2023-06-30formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2023-06-15formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2022-09-30formatting: passedlinting: failed |
1 |
1 |
||
Get projection data from CORDEX |
last update 2023-05-11formatting: failedlinting: failed |
1 |
1 |
||
A pipeline for processing raw Illumina reads to draft assemblies and annotations. |
last update 2023-02-16formatting: failedlinting: passed |
1 |
1 |
||
Example of a straightforward simple snakemake workflow |
last update 2023-05-16formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2023-05-08formatting: failedlinting: failed |
1 |
1 |
||
Maastricht Covid processing pipeline |
last update 2022-11-11formatting: failedlinting: failed |
1 |
0 |
||
Source code accompanying the paper Measures of epitope binding degeneracy from T cell receptor reper… |
last update 2023-06-07formatting: failedlinting: failed |
1 |
1 |
||
Simple Snakemake example |
last update 2022-10-16formatting: failedlinting: passed |
1 |
5 |
||
Adaptive_sampling_Workflow |
last update 2023-06-28formatting: failedlinting: failed |
1 |
2 |
||
Acceptance testing and comparison for lachesis crate |
last update 2023-04-26formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2023-03-29formatting: failedlinting: failed |
1 |
3 |
||
Snippet for snakemake pipelines |
last update 2023-05-08formatting: failedlinting: failed |
1 |
1 |
||
Mendelian Randomization pipeline |
mendelian-randomization snakemake pipeline |
last update 2023-04-14formatting: failedlinting: failed |
1 |
1 |
|
Snakemake workflow for aligning targeted Illumina sequencing data |
last update 2023-05-02formatting: failedlinting: failed |
1 |
3 |
||
pipeline 5mC site identification on a genome assembly from hifi reads |
last update 2023-06-30formatting: failedlinting: passed |
1 |
1 |
||
No description available. |
last update 2022-03-23formatting: failedlinting: failed |
1 |
2 |
||
Code for MinION Plasmid Sequence Verification pipeline |
last update 2023-04-27formatting: failedlinting: failed |
1 |
1 |
||
Demonstrating an RNA-seq workflow in Snakemake. |
last update 2023-06-28formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2023-01-17formatting: failedlinting: failed |
1 |
2 |
||
Code for the pre-trained reference models uploaded to scvi-hub on HuggingFace |
last update 2023-05-19formatting: failedlinting: passed |
1 |
4 |
||
A simple example snakemake workflow |
last update 2023-05-26formatting: failedlinting: failed |
1 |
1 |
||
A Snakemake workflow to cluster proteins using MMseqs2 |
last update 2023-03-07formatting: passedlinting: failed |
1 |
1 |
||
No description available. |
last update 2022-10-04formatting: failedlinting: failed |
1 |
1 |
||
Snakemake workflow to generate figures and results from GAMBIT paper |
last update 2022-07-19formatting: failedlinting: failed |
1 |
1 |
||
3º Lugar: Desafio LBB-Mendelics 2021. https://github.com/mendelics/lbb-mendelics-2021 |
last update 2023-02-18formatting: failedlinting: failed |
1 |
1 |
||
Snakemake single-cell multiome analysis pipeline |
last update 2023-02-21formatting: failedlinting: failed |
1 |
0 |
||
No description available. |
last update 2023-02-16formatting: failedlinting: failed |
1 |
2 |
||
No description available. |
last update 2023-02-15formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2022-11-08formatting: failedlinting: failed |
1 |
1 |
||
Whole genome tree sequence analyses |
last update 2022-11-07formatting: passedlinting: passed |
1 |
2 |
||
Snakemake workflow for processing Mycobacterium leprae whole genome sequencing data |
bacterial-genomes genomics mycobacteria |
last update 2023-03-10formatting: failedlinting: failed |
1 |
0 |
|
Discovery of siRNA regions and small RNA tail quantification |
last update 2022-07-14formatting: failedlinting: failed |
1 |
2 |
||
clinical-genomics-uppsala/wgs_leukemia_tumor_only_konigskobra |
Snakemake workflow to analyse hematological malignancies in whole genome data |
last update 2023-03-13formatting: failedlinting: failed |
1 |
2 |
|
Synchronize public DNAm array data. This resource provides a full Snakemake workflow to download, ha… |
last update 2022-08-02formatting: failedlinting: failed |
1 |
4 |
||
No description available. |
last update 2022-12-15formatting: failedlinting: failed |
1 |
3 |
||
No description available. |
last update 2022-11-01formatting: failedlinting: failed |
1 |
1 |
||
A pipeline for TotalRNA analysis |
last update 2022-12-15formatting: passedlinting: failed |
1 |
1 |
||
Bulk RNA seq analysis pipeline for tumor infiltrating lymphocytes between the control, VP16 and CPT1… |
last update 2022-11-08formatting: failedlinting: failed |
1 |
2 |
||
Step-by-step instructions and Snakemake pipeline for processing Replication Timing Data |
bioinformatics genomics ngs pipeline dna-replication |
last update 2022-08-31formatting: failedlinting: failed |
1 |
0 |
|
A snakemake pipeline that performs variant calling of Nanopore reads from FastQ files for non-model … |
genomics bioinformatics-pipeline snakemake-workflows snvs variant variant-calling |
last update 2022-12-12formatting: failedlinting: failed |
1 |
1 |
|
Phylogenomics tutorial based on BUSCO genes |
last update 2022-06-24formatting: failedlinting: failed |
1 |
1 |
||
Design clade-specific primers targeting a pan-genome core gene |
archaea bacteria bioinformatics primer-design primers |
last update 2022-08-19formatting: failedlinting: failed |
1 |
3 |
|
Automated variant calling |
last update 2023-01-06formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2022-07-28formatting: failedlinting: passed |
1 |
11 |
||
No description available. |
last update 2022-08-19formatting: failedlinting: failed |
1 |
2 |
||
No description available. |
last update 2022-09-02formatting: failedlinting: failed |
1 |
1 |
||
Sampling sequencing reads, running sherman and running bismark. Resulting bam file is used as simula… |
last update 2022-09-07formatting: failedlinting: failed |
1 |
1 |
||
singularity & snakemake workflow for trancriptomic analyses of Aechmea species. |
transcriptomics |
last update 2022-09-29formatting: failedlinting: failed |
1 |
1 |
|
Final project submission for the 2020 programming course at UZH. Downloads and visualizes ZVV timeta… |
last update 2022-10-06formatting: failedlinting: failed |
1 |
1 |
||
Some test with SagE and Orderby limit k |
last update 2022-07-25formatting: failedlinting: failed |
1 |
1 |
||
A repository for RNA-seq workflow |
snakemake-rna-seq fpkm gene snakemake-pipeline rna-seq-data rna-seq-analysis rna-seq-pipeline |
last update 2022-09-16formatting: failedlinting: failed |
1 |
0 |
|
No description available. |
last update 2022-10-28formatting: failedlinting: failed |
1 |
2 |
||
Design target-specific probe pairs for split-HCR and other split encoding probe amplification readou… |
last update 2022-02-25formatting: failedlinting: failed |
1 |
2 |
||
A simple and entertaining introduction to Snakemake workflows. |
snakemake shakespeare fun |
last update 2022-07-29formatting: failedlinting: failed |
1 |
0 |
|
Analysis pipeline for CUT&RUN Data. Currently configured for use in the McKay Lab at UNC, but extens… |
last update 2022-07-22formatting: failedlinting: failed |
1 |
2 |
||
Metabarcoding Pipeline |
last update 2021-03-23formatting: failedlinting: failed |
1 |
2 |
||
Simplified SAMap workflow |
last update 2022-02-04formatting: failedlinting: failed |
1 |
3 |
||
Repository reimplementing the Lei Duan et al. (2022) study and model advanced nuclear from here (htt… |
last update 2022-07-10formatting: failedlinting: failed |
1 |
1 |
||
Processing pipeline for public multiome and scATAC-seq immune datasets |
last update 2022-06-28formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2022-08-17formatting: passedlinting: passed |
1 |
4 |
||
Bioinformatics pipeline for processing 16s marker gene metagenomic sequence data. |
last update 2022-06-27formatting: failedlinting: failed |
1 |
1 |
||
ebi-gene-expression-group/cross-species-cellgroup-comparison |
Development project for comparing cell groupings between experiments across species |
last update 2022-06-06formatting: failedlinting: failed |
1 |
4 |
|
No description available. |
last update 2022-06-13formatting: failedlinting: failed |
1 |
1 |
||
scNOVA : Single-Cell Nucleosome Occupancy and genetic Variation Analysis |
single-cell-multiomics structural-variation chromatin-accessibiity nucleosome cancer-genomics |
last update 2022-01-15formatting: failedlinting: failed |
1 |
1 |
|
Python implementation of ARIO model |
last update 2022-09-07formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2021-12-28formatting: failedlinting: failed |
1 |
1 |
||
Second workflow that takes the output of the guppy workflow to run fastqc and create a multiQC repor… |
last update 2022-05-31formatting: failedlinting: failed |
1 |
2 |
||
Tools and utilities for making use of mastiff |
last update 2022-08-28formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2022-04-30formatting: failedlinting: failed |
1 |
1 |
||
deepvariant snakemake wrapper |
last update 2022-04-30formatting: failedlinting: failed |
1 |
1 |
||
A Snakemake script for automation of the metaWRAP modules |
last update 2022-04-07formatting: failedlinting: failed |
1 |
2 |
||
snakemake files of the tuxedo v2 pipeline from Pertea et al 2016 |
snakemake tuxedo2 samtools hisat2 stringtie ballgown rskittlebrewer r smsk differential expression rnaseq rna-seq conda conda-environment |
last update 2022-04-05formatting: failedlinting: failed |
1 |
2 |
|
Annotates sequences with Eggnog-mapper and hhblits against PDB70 |
last update 2022-04-05formatting: failedlinting: failed |
1 |
1 |
||
A subsampling method for large-scale SARS-CoV-2 genome data sets |
sars-cov-2 subsampling |
last update 2022-05-20formatting: failedlinting: failed |
1 |
1 |
|
Quantify HERVs in PBMC datasets using single-cell Telescope (scTelescope) |
last update 2022-04-16formatting: failedlinting: failed |
1 |
0 |
||
No description available. |
last update 2022-01-28formatting: failedlinting: failed |
1 |
1 |
||
A snakemake workflow wrapping various phage host prediction tools |
phage-host-prediction bioinformatics-pipeline |
last update 2021-11-23formatting: failedlinting: failed |
1 |
1 |
|
RNAseq workflow for Beowulf based on STAR |
last update 2022-06-07formatting: failedlinting: failed |
1 |
1 |
||
TimeAdapt makes a joint inference of demography and selection from longitudinal population genomic d… |
last update 2021-12-16formatting: failedlinting: failed |
1 |
1 |
||
Mapping mutations to the SARS-CoV-2 B.1.351 RBD that reduce binding of polyclonal plasmas from B.1.3… |
last update 2022-02-14formatting: failedlinting: failed |
1 |
0 |
||
Whole exome somatic copy number analysis with Sequenza and CNVKit |
last update 2022-02-28formatting: failedlinting: failed |
1 |
1 |
||
This a snakemake pipeline to detect Somatic mutations (GATK4 and Mutect2) |
somatic mutations snakemake mutect2 gatk4 |
last update 2022-02-25formatting: failedlinting: failed |
1 |
1 |
|
Extract set of tandem poly(A) sites from the PolyASite atlas. |
bioinformatics snakemake polyadenylation |
last update 2021-12-10formatting: failedlinting: failed |
1 |
4 |
|
Bacterial GWAS for E. coli BSI genetic determinants |
last update 2022-01-14formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2021-10-12formatting: failedlinting: failed |
1 |
4 |
||
No description available. |
last update 2021-11-05formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2022-04-08formatting: failedlinting: failed |
1 |
3 |
||
Snakemake workflow to perform GATK’s best practices for Germline SNP & Indel Discovery in Whole Gen… |
last update 2022-01-10formatting: failedlinting: failed |
1 |
2 |
||
simulation of E. coli chemoreceptor array dynamics |
last update 2022-01-10formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2022-01-07formatting: failedlinting: failed |
1 |
1 |
||
Accompanying repository for master’s thesis: https://scholarworks.sjsu.edu/etd_projects/1055/ |
last update 2022-03-02formatting: failedlinting: failed |
1 |
2 |
||
No description available. |
last update 2021-12-13formatting: failedlinting: failed |
1 |
2 |
||
nnUnet training workflow for fetal bold MRI |
last update 2021-12-06formatting: failedlinting: failed |
1 |
1 |
||
Term Project for BIOF 501 UBC |
last update 2021-12-29formatting: failedlinting: failed |
1 |
1 |
||
A two-step model that combines neural network and ensemble learning to predict OCR–mediated interact… |
deep-learning chromatin-accessibiity hic loops interaction de-novo-prediction |
last update 2022-01-07formatting: failedlinting: failed |
1 |
1 |
|
bug demonstration for snakemake-github-action containerize task |
last update 2021-11-25formatting: failedlinting: failed |
1 |
1 |
||
Snakefile pipeline for taxonomic and functional annotation of (Metagenome assembled) genome |
last update 2020-11-30formatting: failedlinting: failed |
1 |
2 |
||
CPTAC RNA expression pipeline |
last update 2021-12-07formatting: failedlinting: failed |
1 |
21 |
||
A bioinformatics tutorial demonstrating the application of long read cDNA sequence data for the iden… |
last update 2021-10-21formatting: failedlinting: failed |
1 |
1 |
||
Code that attempts to reproduce A Reproducible MEG/EEG Group Study With the MNE Software by Jas et a… |
last update 2021-10-06formatting: failedlinting: failed |
1 |
2 |
||
Hybrid genome assembly of Acanthamoeba castellanii. Combining long reads, Hi-C and shotgun. |
last update 2022-02-17formatting: failedlinting: failed |
1 |
2 |
||
No description available. |
last update 2021-09-29formatting: failedlinting: failed |
1 |
1 |
||
Snakemake workflow to characterize the presence and abundance of antibiotic resistance genes in meta… |
last update 2021-11-15formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2021-09-03formatting: failedlinting: failed |
1 |
1 |
||
Supplementary material for the OLOGRAM-MODL paper |
last update 2021-09-01formatting: failedlinting: failed |
1 |
2 |
||
No description available. |
last update 2022-01-20formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2021-09-11formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2021-10-05formatting: failedlinting: failed |
1 |
1 |
||
A Snakemake pipeline for RRBS data analysis |
bioinformatics-pipeline methylation rrbs-pipeline snakemake rrbs-data-analysis |
last update 2021-08-26formatting: failedlinting: failed |
1 |
1 |
|
Goal is to reproduce the Nanoseq Bioinformatics pipeline described here (https://github.com/nf-core/… |
last update 2021-08-20formatting: failedlinting: failed |
1 |
2 |
||
The snakemake tutorial run with spack! (under development) |
last update 2021-08-17formatting: failedlinting: failed |
1 |
2 |
||
Snakemake Implementation of RecSearch featured in Pervasive duplication of tumor suppressors in Afro… |
petosparadox biology reproducible-research reproducible-paper cancer evolution comparative-genomics elephant manatee |
last update 2021-08-16formatting: failedlinting: failed |
1 |
0 |
|
A Snakemake workflow for running and analysing polymer simulations using Polychrom. |
last update 2021-07-26formatting: failedlinting: failed |
1 |
1 |
||
Snakemake workflow for CNV detection on exome and custom target panel sequencing data |
last update 2021-07-23formatting: failedlinting: passed |
1 |
2 |
||
Phylogenomics tutorial based on BUSCO genes |
last update 2021-07-09formatting: failedlinting: failed |
1 |
1 |
||
GTEx isoform expression queries for transcription factors in human hypothalamus. |
last update 2021-07-06formatting: failedlinting: failed |
1 |
0 |
||
A computational method to generate causal explanations for proteomic profiles using prior mechanisti… |
last update 2021-06-22formatting: failedlinting: failed |
1 |
3 |
||
Analyzing linguistic data from the Hebrew Bible in conjunction with Gesenius |
last update 2021-06-11formatting: failedlinting: failed |
1 |
0 |
||
No description available. |
last update 2021-06-08formatting: failedlinting: failed |
1 |
12 |
||
A snakemake pipeline for performing read and assembly based shotgun metagenomics from QC to statisti… |
last update 2021-05-19formatting: failedlinting: failed |
1 |
1 |
||
snakemake workflow for basecalling and demultiplexing of ONT sequencing data |
snakemake-workflow basecalling demultiplexing nanopore |
last update 2021-04-08formatting: failedlinting: failed |
1 |
3 |
|
Outlier prediction-based solution to Task1 of the End ALS Kaggle challenge |
last update 2021-05-16formatting: failedlinting: failed |
1 |
5 |
||
CGR’s QIIME microbiome pipeline |
last update 2021-05-12formatting: failedlinting: failed |
1 |
4 |
||
No description available. |
last update 2019-04-15formatting: failedlinting: failed |
1 |
1 |
||
Snakemake-based pipeline for analyzing the V4 region of the 16S rRNA gene with mothur. |
last update 2020-08-17formatting: failedlinting: failed |
1 |
2 |
||
Creating a variant calling pipeline |
last update 2020-09-10formatting: failedlinting: failed |
1 |
1 |
||
Snakemake rules for parallel QC of shotgun data |
last update 2018-05-15formatting: failedlinting: failed |
1 |
2 |
||
Rules for CASINO tasks |
last update 2019-09-08formatting: failedlinting: failed |
1 |
2 |
||
Generalized Snakemake workflow for R.4Cker |
last update 2016-10-25formatting: failedlinting: failed |
1 |
0 |
||
AMBIC Epigenomics project analysis |
last update 2020-10-22formatting: failedlinting: failed |
1 |
2 |
||
Workflow for MAG construction |
last update 2020-01-28formatting: failedlinting: failed |
1 |
2 |
||
Estimate fastq-formatted read abundace in RNA-Seq analysis with Kallisto |
snakemake-workflow snakemake bioinformatics reproducible-workflows kallisto fastqc multiqc conda json-schema |
last update 2020-02-24formatting: failedlinting: failed |
1 |
1 |
|
A workflow designed to clean fastq files for the SEACONNECT project |
fastq qc preprocessing filtering snakemake quality ngs bioinformatics illumina cleaning singularity docker workflow container trimming chastity quality-filtering phred-quality-scores sequencing contaminants |
last update 2019-11-20formatting: failedlinting: failed |
1 |
1 |
|
Example workflow using snakemake |
last update 2020-10-28formatting: failedlinting: failed |
1 |
1 |
||
A basic boilerplate structure for snakemake based pipelines. |
snakemake conda codingene |
last update 2020-06-19formatting: failedlinting: failed |
1 |
0 |
|
snakemake pipeline to generate art_illumina profiles from public datasets |
last update 2020-05-20formatting: failedlinting: failed |
1 |
5 |
||
Finding virus integration sites from whole genome nanopore sequence |
last update 2021-04-05formatting: failedlinting: failed |
1 |
1 |
||
Kallisto Bus for 10X |
last update 2020-06-23formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2020-09-01formatting: failedlinting: failed |
1 |
2 |
||
A snakemake workflow for the OrthoEvol python package. |
snakemake snakemake-workflow snakemake-pipelines orthology-inference orthoevol |
last update 2019-07-08formatting: failedlinting: failed |
1 |
2 |
|
A Snakemake workflow for the chain of models approach to hydrologic modeling |
last update 2019-09-12formatting: failedlinting: failed |
1 |
1 |
||
Snakemake workflow for processing pdx exome data. |
last update 2018-01-29formatting: failedlinting: failed |
1 |
1 |
||
snakemake snp calling pipeline based on freebayes |
last update 2019-07-19formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2020-07-16formatting: failedlinting: failed |
1 |
5 |
||
A quality control pipeline for Oxford Nanopore sequencing |
last update 2021-04-28formatting: failedlinting: failed |
1 |
3 |
||
A simple Snakemake workflow to perform network analyses using the Python Geneset Network Analysis (P… |
last update 2020-06-29formatting: failedlinting: failed |
1 |
1 |
||
Snakemake pipeline for paired-end sanger sequences of 16s rRNA |
last update 2020-09-16formatting: failedlinting: failed |
1 |
0 |
||
Pipeline running ‘salmon alevin’ for CITE-seq data |
last update 2020-06-16formatting: failedlinting: failed |
1 |
1 |
||
Arquivos e códigos em bash, R e Python para confecção da minha tese de doutorado. |
last update 2021-03-15formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2020-11-23formatting: failedlinting: failed |
1 |
1 |
||
Snakemake workflow to process and analyse Bisulfite-Sequencing data |
last update 2021-04-23formatting: failedlinting: failed |
1 |
1 |
||
snakemake workflows for processing TCGA RNA-Seq data for the CAMDA2019 challenge |
last update 2021-01-19formatting: failedlinting: failed |
1 |
1 |
||
WORK IN PROGRESS! |
last update 2021-01-05formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2019-07-14formatting: failedlinting: failed |
1 |
1 |
||
High throughput Next Generation Sequencing (NGS) data analysis using Python 3 Snakemake |
last update 2020-12-16formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2018-10-08formatting: failedlinting: failed |
1 |
1 |
||
Perform Cytoscans/Oncoscans CNV analysis with EaCoN |
last update 2021-04-02formatting: failedlinting: failed |
1 |
1 |
||
Dosage Compensation Analyses Pipeline using Snakemake |
last update 2020-09-17formatting: failedlinting: failed |
1 |
0 |
||
Notes on Snakemake |
last update 2019-02-24formatting: failedlinting: failed |
1 |
1 |
||
No description available. |
last update 2025-03-05formatting: failedlinting: failed |
0 |
1 |
||
This pipeline will process the files after deep WES, to see if there are any mutations in the somati… |
last update 2025-03-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-03-05formatting: failedlinting: failed |
0 |
1 |
||
Growth rates of influenza viruses with HAs in H3 2023-2024 sequencing-based neutralization libraries |
last update 2025-03-04formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2025-03-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-03-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-03-04formatting: failedlinting: failed |
0 |
1 |
||
A pipeline to gather snoRNA and RBP interactions to perform a snoRNA-RBP interaction network analysi… |
last update 2025-03-04formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2025-03-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-03-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-03-04formatting: failedlinting: failed |
0 |
1 |
||
Just annotate the MAGs as in mg_assembly |
last update 2025-03-04formatting: passedlinting: failed |
0 |
1 |
||
miRA - miRNA Analysis |
last update 2025-03-04formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-03-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-03-04formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2025-03-03formatting: failedlinting: failed |
0 |
2 |
||
Snakemake workflow for benchmarking FiPy solvers |
last update 2025-03-03formatting: failedlinting: failed |
0 |
1 |
||
RNA Sequencing Data Analysis: A 2025 Review and Updated Snakemake Pipeline |
rnaseq-analysis snakemake-workflow |
last update 2025-03-03formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2025-03-03formatting: failedlinting: failed |
0 |
1 |
||
A pipeline to clean short eukaryotic amplicon datasets after dada2 processing. |
last update 2025-03-03formatting: failedlinting: failed |
0 |
1 |
||
DNAseq pipeline |
last update 2025-03-07formatting: failedlinting: failed |
0 |
1 |
||
End-to-End Pipeline for Bulk RNA Seq Data Processing |
last update 2025-03-07formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for RNA-Seq and TGIRT-Seq |
last update 2025-03-07formatting: passedlinting: failed |
0 |
1 |
||
Basic RNA-seq snakemake workflow. Use as a module for larger workflows. |
last update 2025-03-06formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-03-06formatting: failedlinting: failed |
0 |
1 |
||
Snakemake Pipeline with selectable modules |
last update 2025-03-06formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2025-03-06formatting: failedlinting: failed |
0 |
1 |
||
Accompanying Github repository to the Paper Gregor et al. (in prep). |
last update 2025-03-06formatting: failedlinting: passed |
0 |
1 |
||
Kraken2 + Bracken based pipeline for classifying and quantifying microbial reads from GDC TCGA WGS d… |
bioinformatics-pipeline bioinformatics-workflow metagenomic-pipeline metagenomics metagenomics-taxon-profiling snakemake-pipeline snakemake-workflow |
last update 2025-03-06formatting: passedlinting: failed |
0 |
1 |
|
No description available. |
last update 2025-03-06formatting: failedlinting: failed |
0 |
1 |
||
Lightweight version of the TAR-scRNA-seq pipeline, redesigned to be barebones and more flexible |
last update 2025-03-06formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for whole-exome sequencing |
last update 2025-03-06formatting: failedlinting: failed |
0 |
2 |
||
Pipeline of the anlysis of the honeybee gut bacteriome and virome. |
last update 2025-03-06formatting: failedlinting: failed |
0 |
1 |
||
A snakemake pipeline for de novo hybrid assembly in barley using Oxford Nanopore and Illumina reads |
last update 2025-03-06formatting: passedlinting: passed |
0 |
1 |
||
Mapping of shotgun sequencing data against the UNITE database |
last update 2025-03-06formatting: failedlinting: failed |
0 |
0 |
||
Whole exome sequencing pipeline for inherited diseases |
last update 2025-03-06formatting: failedlinting: failed |
0 |
3 |
||
Clinical Genomics Uppsala inheritance disease pipeline for WGS |
last update 2025-03-06formatting: failedlinting: failed |
0 |
0 |
||
(Pre-release) Bootstrap resample your low-powered RNA-Seq data set to estimate the expected reliabil… |
last update 2025-03-06formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-03-05formatting: failedlinting: failed |
0 |
8 |
||
A pipeline that facilitates the CRISPR analysis |
last update 2025-03-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-03-05formatting: failedlinting: failed |
0 |
1 |
||
This is the repository of the pipeline META-DIFF, which detects sequences in differential abundances… |
annotation bioinformatics-pipeline kmers metagenomics shotgun-pipeline snakemake |
last update 2025-03-05formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2025-03-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-03-10formatting: failedlinting: failed |
0 |
1 |
||
A pipeline for comprehensive analysis of gene duplicates in eukaryotic genomes |
last update 2025-03-10formatting: failedlinting: failed |
0 |
1 |
||
Repository for all the code created for the TreeSAPP Capstone 2025 collaboration |
last update 2025-03-10formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2025-03-10formatting: passedlinting: failed |
0 |
1 |
||
Profiling PROTAX-fungi for quick and coarse classification of ITS metabarcoding reads |
last update 2025-03-09formatting: failedlinting: failed |
0 |
5 |
||
No description available. |
last update 2025-03-09formatting: failedlinting: failed |
0 |
1 |
||
The workflow used for the experiments of the paper: Faster Inference of Cell Complexes from Flows vi… |
last update 2025-03-09formatting: failedlinting: failed |
0 |
2 |
||
A Snakemake workflow for analyzing RNA crosslinking and proximity ligation data using DuplexDiscover… |
last update 2025-03-09formatting: failedlinting: failed |
0 |
1 |
||
La idea es crear una página web con especies de fauna y flora de Gran Canaria que vaya encontrando, … |
last update 2025-03-09formatting: failedlinting: failed |
0 |
1 |
||
Tiempo de Canarias basado en los datos abiertos de IDECanarias |
last update 2025-03-09formatting: failedlinting: failed |
0 |
1 |
||
TEA is short for Transposable Element Analysis. It is a user-friendly TE family differential abundan… |
last update 2025-03-08formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-03-07formatting: failedlinting: failed |
0 |
1 |
||
Sanekamke workflow used to align reads with STAR |
last update 2025-03-07formatting: passedlinting: passed |
0 |
1 |
||
No description available. |
last update 2025-03-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-03-07formatting: failedlinting: failed |
0 |
5 |
||
Post-mapping analysis of DNA methylation sequencing data |
last update 2025-03-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-25formatting: failedlinting: failed |
0 |
1 |
||
🧬 Automated short-read bacterial genome assembly and analysis tool implemented in Snakemake. |
last update 2025-02-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-25formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-24formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-24formatting: failedlinting: failed |
0 |
1 |
||
pull homologous region and gene of interest from a list of query haplotypes |
last update 2025-02-24formatting: failedlinting: failed |
0 |
1 |
||
This repository is only meant for testing out the required minimal permissions to get GitHub Actions… |
last update 2025-02-24formatting: failedlinting: passed |
0 |
1 |
||
Snakemake workflow for the assembly and evaluation of bovine genomes. |
bioinformatics bioinformatics-pipeline biology bovine genome genome-analysis genome-annotation genome-assembly genomics |
last update 2025-02-24formatting: failedlinting: failed |
0 |
1 |
|
Phylogenetics and recombination analysis of Enterovirus C with a focus on vaccine-derived poliovirus… |
last update 2025-02-24formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-24formatting: failedlinting: failed |
0 |
4 |
||
No description available. |
last update 2025-02-24formatting: failedlinting: failed |
0 |
1 |
||
Visualise SARS-CoV-2 amplicon dropout |
last update 2025-02-24formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-28formatting: passedlinting: failed |
0 |
1 |
||
Here be dragons. |
last update 2025-02-28formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2025-02-27formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2025-02-27formatting: failedlinting: failed |
0 |
1 |
||
Collection of analysis scripts and notebooks related to regulated cell death |
bash cancer multi-omics python r rna-seq rna-seq-analysis sequence-mapping transcript-quantification transcriptomics |
last update 2025-02-27formatting: failedlinting: failed |
0 |
1 |
|
High-level repo for using KAPy in combination with custom MET code |
last update 2025-02-27formatting: failedlinting: failed |
0 |
4 |
||
WDL & Snakemake workflows to perform comprehensive RNA protein binding motif analysis |
last update 2025-02-27formatting: passedlinting: failed |
0 |
1 |
||
This workflow performs trimming, alignment, and generates BigWig and BED files for CUT&Tag data. The… |
last update 2025-02-27formatting: failedlinting: failed |
0 |
2 |
||
Pipeline to align 10x multiome fastq files and demultiplex |
last update 2025-02-26formatting: failedlinting: failed |
0 |
4 |
||
No description available. |
last update 2025-02-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-26formatting: failedlinting: failed |
0 |
1 |
||
Snakemake installation for Stanage HPC |
last update 2025-02-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-26formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake Pipeline to Output meTagenomics-derived Biosynthetic Gene Clusters |
last update 2025-02-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-26formatting: failedlinting: failed |
0 |
1 |
||
ASTRA for single cell data analysis |
last update 2025-02-26formatting: failedlinting: failed |
0 |
2 |
||
Parallel pygwb pipeline for Reana using ET MDC data. |
last update 2025-02-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-26formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2025-03-02formatting: failedlinting: failed |
0 |
1 |
||
data processing |
last update 2025-03-02formatting: failedlinting: passed |
0 |
0 |
||
Tool for evaluating k-mer feature importance for classification of biological sequences. |
last update 2025-03-02formatting: failedlinting: failed |
0 |
1 |
||
Introduction to snakemake as a workflow management tool |
last update 2025-03-02formatting: passedlinting: passed |
0 |
2 |
||
No description available. |
last update 2025-03-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-03-01formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-03-01formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2025-02-28formatting: failedlinting: failed |
0 |
4 |
||
A Snakemake workflow for clustering billions and billions of proteins |
last update 2025-02-28formatting: failedlinting: failed |
0 |
1 |
||
This is the repository for analysis of the PLETHORA-driving GRN in the RAM of Arabidopsis and other … |
last update 2025-02-28formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for mTags extraction and classification |
last update 2025-02-28formatting: failedlinting: failed |
0 |
1 |
||
Perform a benchmark comparing mt-scite to scite and merlin. |
last update 2025-02-28formatting: failedlinting: failed |
0 |
1 |
||
This Snakemake workflow includes the creation of chain file, Liftover, Phasing and Imputation, as we… |
last update 2025-02-18formatting: failedlinting: failed |
0 |
1 |
||
A workflow to train a convolutional neural network with SLiM outputs |
last update 2025-02-17formatting: failedlinting: failed |
0 |
1 |
||
Shell scripts for prototyping a QIIME2 |
last update 2025-02-17formatting: failedlinting: failed |
0 |
3 |
||
Snakemake workflow to basecall ONT reads with dorado. |
last update 2025-02-17formatting: failedlinting: failed |
0 |
1 |
||
Processing for the Gonzo gMRI dataset |
last update 2025-02-17formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2025-02-17formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-21formatting: failedlinting: failed |
0 |
1 |
||
Code to generate the data and website for Rat TWAS Hub |
genetics genomics gwas rats twas |
last update 2025-02-21formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2025-02-21formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-20formatting: failedlinting: passed |
0 |
1 |
||
This repository is to store everything around my master thesis |
last update 2025-02-20formatting: passedlinting: failed |
0 |
1 |
||
Revisiting Adaptive Introgression at the HLA Genes in Lithuanian Genomes with Machine Learning |
last update 2025-02-20formatting: failedlinting: failed |
0 |
1 |
||
Manuscript associated with StrainPGC tool for gene content estimation |
last update 2025-02-20formatting: passedlinting: failed |
0 |
2 |
||
HyperLogLog-based first-fit bin packing for genomes |
last update 2025-02-20formatting: failedlinting: failed |
0 |
1 |
||
Pipeline for running data processing and preparation for Ploidetect |
last update 2025-02-19formatting: passedlinting: failed |
0 |
5 |
||
Analysis workflow for 2024 antisymmetric Sp(4) paper |
last update 2025-02-19formatting: failedlinting: failed |
0 |
2 |
||
ASTRA for bulk data analysis |
last update 2025-02-19formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2025-02-19formatting: failedlinting: failed |
0 |
1 |
||
Run Recount-pump with snakemake workflow interface and conda deployment |
last update 2025-02-19formatting: failedlinting: failed |
0 |
1 |
||
ERMA - epicPCR Resistome-Microbiome Analyzer |
last update 2025-02-19formatting: failedlinting: failed |
0 |
1 |
||
Add-on and config for Poppy running Twist Myeloid panel |
last update 2025-02-19formatting: failedlinting: failed |
0 |
3 |
||
RΔD (Rapid Δ Detecter) is a workflow for fast and efficient identification of deletions in targeted … |
last update 2025-02-23formatting: failedlinting: failed |
0 |
1 |
||
RΔD (Rapid Δ Detecter) is a workflow for fast and efficient identification of deletions in targeted … |
last update 2025-02-23formatting: failedlinting: failed |
0 |
0 |
||
A thin wrapper to simplify running cellprofiler on della |
last update 2025-02-22formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2025-02-22formatting: failedlinting: failed |
0 |
0 |
||
Basic scripts for creating an oligo design file |
last update 2025-02-21formatting: passedlinting: failed |
0 |
2 |
||
DISCO Processing pipeline for Copenhagen by IRT SystemX |
last update 2025-02-21formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-11formatting: failedlinting: failed |
0 |
1 |
||
Isolated chromosome sequencing analysis |
last update 2025-02-11formatting: failedlinting: failed |
0 |
2 |
||
Create datasets for quantity span identification and measurement context extraction based on Wikiped… |
last update 2025-02-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-11formatting: failedlinting: failed |
0 |
0 |
||
Reproducible experiments of the scientific paper for The Web Conference 2025. |
last update 2025-02-11formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2025-02-11formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2025-02-10formatting: failedlinting: failed |
0 |
1 |
||
Analyses for performing the single cell RNA-sequencing analyses in the MAPS CRC cohort. |
last update 2025-02-10formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-10formatting: failedlinting: failed |
0 |
2 |
||
Pipeline for preparing shared resources such as aligner index files in the BBC. |
last update 2025-02-10formatting: failedlinting: failed |
0 |
5 |
||
Gene tree-based annotations |
last update 2025-02-10formatting: failedlinting: failed |
0 |
2 |
||
Genome-Function-Initiative-Oxford/scATAC_Pseudoreplicate_Pipeline |
Snakemake pipeline to create scATAC-seq pseudoreplicates |
last update 2025-02-13formatting: failedlinting: failed |
0 |
0 |
|
Infrastructure for static resources used by vdblab-pipelines |
last update 2025-02-13formatting: failedlinting: failed |
0 |
5 |
||
A snakemake workflow for the BD Rhapsody Sequence Analysis Pipeline |
last update 2025-02-13formatting: failedlinting: failed |
0 |
1 |
||
Standard RNAseq analysis pipeline using snakemake. |
fastqc rsem salmon star snakemake rna-seq |
last update 2025-02-12formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2025-02-12formatting: failedlinting: failed |
0 |
1 |
||
Workflow to use stringdecomposer to annotate alpha-satellite HOR monomers. |
last update 2025-02-12formatting: passedlinting: failed |
0 |
0 |
||
A bare repo with snakemake |
last update 2025-02-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-12formatting: failedlinting: failed |
0 |
1 |
||
Techno-Economic Assessment of Green Hydrogen and Battery Energy Storage in an Isolated Power System:… |
last update 2025-02-12formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-12formatting: failedlinting: failed |
0 |
1 |
||
core-unit-bioinformatics/workflow-smk-genome-hybrid-assembly |
No description available. |
last update 2025-02-12formatting: failedlinting: failed |
0 |
1 |
|
core-unit-bioinformatics/project-run-hgsvc-hybrid-assemblies |
Project repository for the HGSVC phase 3 paper |
last update 2025-02-12formatting: failedlinting: failed |
0 |
1 |
|
A snakemake-based 3D-segmentation pipeline taylored for X-ray tomography data. |
last update 2025-02-12formatting: failedlinting: failed |
0 |
1 |
||
Workflow to generate hifiasm and verkko assemblies. |
last update 2025-02-12formatting: passedlinting: failed |
0 |
0 |
||
Snakemake Pipeline for Methylation Detection of Nanopore Sequencing Data using MicrobeMod |
last update 2025-02-16formatting: failedlinting: failed |
0 |
1 |
||
Short Snakemake Pipeline: Bowtie2 Read Mapping and Coverage QC for Illumina short reads. |
last update 2025-02-16formatting: failedlinting: failed |
0 |
1 |
||
Genome Assembly, Binning, Classification, and Gene Annotation Snakemake Pipeline for: Illumina, Oxfo… |
last update 2025-02-16formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-15formatting: failedlinting: failed |
0 |
1 |
||
Workflow to map PacBio HiFi reads back to an assembly and check for misassemblies at specific region… |
last update 2025-02-15formatting: failedlinting: failed |
0 |
0 |
||
Curation of Metabol(om)ic Response to Omnivorous Dietary Patterns Using Randomized Controlled Feedin… |
last update 2025-02-14formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-04formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2025-02-03formatting: failedlinting: failed |
0 |
1 |
||
A streamlined, automated pipeline for protein structure prediction, integrating MODELLER for templat… |
last update 2025-02-03formatting: failedlinting: failed |
0 |
1 |
||
compile a phylogenetic dataset from genewise CDS fasta files |
last update 2025-02-03formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2025-02-06formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2025-02-06formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake pipeline to analyze RNA-seq expression data |
rna-seq-pipeline snakemake-workflow |
last update 2025-02-06formatting: failedlinting: failed |
0 |
1 |
|
A snakemake workflow for amplicon sequencing |
amplicon-sequencing gene-drive genomic-surveillance illumina insecticide-resistance snakemake-workflow |
last update 2025-02-06formatting: failedlinting: failed |
0 |
4 |
|
Benchmarking methods of ATAC-seq pipline |
last update 2025-02-06formatting: failedlinting: failed |
0 |
1 |
||
Used to examine wheater nuclear energy is compatible with the Danish energy system |
last update 2025-02-05formatting: failedlinting: failed |
0 |
1 |
||
zimmmermann-kogadeeva-group/PseudomonasAntibioticsResistance |
No description available. |
last update 2025-02-05formatting: failedlinting: failed |
0 |
1 |
|
Workflow template for Snakemake |
last update 2025-02-05formatting: passedlinting: failed |
0 |
1 |
||
O GetVar é útil para o auxílio a diagnósticos genéticos e aconselhamentos, permitindo decisões basea… |
beta-release genomics-analysis mutation mvp snp-calling variant-analysis |
last update 2025-02-04formatting: failedlinting: failed |
0 |
0 |
|
A machine learning project for the ML Seminar 2024 at the TU Dortmund (faculty of physics). A convol… |
last update 2025-02-09formatting: failedlinting: failed |
0 |
1 |
||
Automated version of APPSquared Pipeline plus updates |
last update 2025-02-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-07formatting: failedlinting: failed |
0 |
1 |
||
A tool designed specifically for analyzing RNA-seq data using Snakemake workflows |
last update 2025-02-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-07formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for Ottawa crime data analysis |
last update 2025-02-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-01-28formatting: passedlinting: failed |
0 |
1 |
||
A streamlined and reproducible Snakemake workflow for batch-correcting RNA-seq gene expression data … |
last update 2025-01-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-01-27formatting: failedlinting: failed |
0 |
2 |
||
Metagenomic pangenome mapper |
last update 2025-01-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-01-30formatting: failedlinting: failed |
0 |
1 |
||
Wow! a ChIP-seq pipeline! |
bioinformatics chip-seq pipeline snakemake |
last update 2025-01-30formatting: failedlinting: failed |
0 |
0 |
|
A Snakemake workflow with associated scripts used for detecting spike NTD repaired deletions in SARS… |
bioinformatics pipeline sars-cov-2 snakemake |
last update 2025-01-31formatting: failedlinting: failed |
0 |
0 |
|
No description available. |
last update 2025-01-30formatting: failedlinting: failed |
0 |
1 |
||
Test of Uniformity for centrosome orientation at early timepoints during Wound Healing Assay |
bioimage-analysis cellprofiler-pipeline fiji-macro-language snakemake-workflow workflow-automation uniformity-tests |
last update 2025-01-30formatting: failedlinting: failed |
0 |
2 |
|
No description available. |
last update 2025-01-29formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-02-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-01-31formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-01-31formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-01-31formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-01-31formatting: failedlinting: failed |
0 |
4 |
||
A Fermi-LAT analysis workflow for reproducible open articles based on showyourwork |
fermi-lat-data fermi-science reproducible-science snakemake showyourwork template |
last update 2025-01-21formatting: failedlinting: failed |
0 |
1 |
|
Snakemake workflow to process circRNA AmpliconSeq datasets generated to study circRNAs in KSHV and h… |
snakemake-workflow amplicon-sequencing amplicon-pipeline circrna circrna-pipeline |
last update 2025-01-21formatting: failedlinting: failed |
0 |
6 |
|
rMATs and IsoformSwitchAnalyeR workflow for multi-group multi-contrasts scenarios |
last update 2025-01-21formatting: failedlinting: failed |
0 |
5 |
||
No description available. |
last update 2025-01-21formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2025-01-21formatting: failedlinting: failed |
0 |
0 |
||
Snakemake pipeline to extract poly(A)-tail containing-reads from RNA-seq alignment files |
last update 2025-01-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-01-20formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake pipeline to process paired-end RAD-Seq data using Stacks |
last update 2025-01-24formatting: failedlinting: failed |
0 |
1 |
||
Workflow for running valleyx on state of california |
last update 2025-01-24formatting: failedlinting: failed |
0 |
1 |
||
Snakemake bioinformatics data processing pipeline template with reproducibility and best practices i… |
last update 2025-01-24formatting: failedlinting: failed |
0 |
1 |
||
The DualRNASeq Pipeline is a comprehensive, automated workflow designed to analyze host-pathogen dua… |
bioinformatics-pipeline dualrna-seq host-pathogen-interactions infection rna-seq snakemake-pipeline |
last update 2025-01-23formatting: failedlinting: failed |
0 |
1 |
|
A sophisticated bioinformatics pipeline for bacterial pangenome analysis, integrating WGS and RNA-Se… |
bioinformatics-pipeline host-pathogen-interactions pangenomics rnaseq snakemake whole-genome-sequencing pan-transcriptomics |
last update 2025-01-23formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2025-01-23formatting: failedlinting: failed |
0 |
1 |
||
Generation of Naegleria fowleri consensus sequences from paired-end reads of cerebrospinal fluid sam… |
last update 2025-01-22formatting: passedlinting: failed |
0 |
1 |
||
A detailed metagenomics workflow for analysis Illumina reads processed from wildlife samples collect… |
last update 2025-01-22formatting: passedlinting: failed |
0 |
1 |
||
TRANQUIL (TRna AbundaNce QUantification pIpeLine) |
last update 2025-01-21formatting: failedlinting: failed |
0 |
5 |
||
Snakemake pipeline containing a feature selection workflow |
last update 2025-01-24formatting: passedlinting: failed |
0 |
1 |
||
An example workflow with snakemake |
last update 2025-01-24formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-01-24formatting: failedlinting: failed |
0 |
1 |
||
Pipeline for automatic analysis of scRNAseq data with the Seurat package |
last update 2025-01-24formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2025-01-14formatting: failedlinting: failed |
0 |
1 |
||
GETVar 🧬👨🏻💻 [DO NOT USE THIS VERSION ⚠️] - THE UPDATED AND FUCTIONAL VERSION IS AVAILABLE ON: https… |
alpha-beta-pruning not-working testing |
last update 2025-01-14formatting: failedlinting: failed |
0 |
1 |
|
Pipeline to predict HiC matrices from ATAC-seq fastq files using maxATAC and C.Origami |
last update 2025-01-13formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2025-01-13formatting: passedlinting: failed |
0 |
1 |
||
Snakemake single-cell RNA-seq data processing pipeline with STAR Solo |
last update 2025-01-13formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for mitochondrial analysis using gatk best practices |
last update 2025-01-15formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-01-15formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-01-14formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-01-18formatting: failedlinting: failed |
0 |
1 |
||
Find single-stranded DNA breaks with an error-prone DNA polymerase |
last update 2025-01-17formatting: failedlinting: failed |
0 |
5 |
||
No description available. |
last update 2025-01-17formatting: failedlinting: failed |
0 |
1 |
||
Pipleline for deep centromeres analysis with CENdetectHOR |
last update 2025-01-10formatting: failedlinting: failed |
0 |
1 |
||
Example of using KAPy in a local setting |
last update 2025-01-10formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-01-10formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2025-01-09formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2025-01-09formatting: failedlinting: failed |
0 |
4 |
||
Snakemake module containing processing steps that should be performed before sequence alignment. |
last update 2025-01-09formatting: failedlinting: failed |
0 |
2 |
||
Collection of rules used to call snv and small indels. |
last update 2025-01-09formatting: failedlinting: failed |
0 |
4 |
||
No description available. |
last update 2025-01-09formatting: failedlinting: failed |
0 |
4 |
||
fusions |
last update 2025-01-09formatting: failedlinting: failed |
0 |
4 |
||
Snakemake module containing different analyses provided by parabricks. |
last update 2025-01-09formatting: failedlinting: failed |
0 |
3 |
||
A fully automated and optimized workflow for REMD simulations, integrating GROMACS, Python, and Snak… |
last update 2025-01-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-16formatting: failedlinting: passed |
0 |
0 |
||
No description available. |
last update 2024-12-15formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-15formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-15formatting: failedlinting: failed |
0 |
1 |
||
the Dip-C snakemake workflow |
last update 2024-12-15formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-12-14formatting: failedlinting: failed |
0 |
1 |
||
Workflow to setup and run CLM cases then analyze the outputs |
last update 2024-12-14formatting: failedlinting: failed |
0 |
1 |
||
Pipeline for SIT data postprocessing |
last update 2024-12-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-13formatting: failedlinting: failed |
0 |
1 |
||
Workflow to generate data starter kits |
last update 2024-12-18formatting: failedlinting: failed |
0 |
3 |
||
A Snakemake pipeline for copy number variant calling without normal tissue samples |
bioinformatics bwa cna cnv cnvkit conda copynumbervariation mutect2 panels purecn sequencing-data snakemake targeted-sequencing |
last update 2024-12-18formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2024-12-17formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow that uses Fractal Zarr thresholding module |
last update 2024-12-17formatting: failedlinting: failed |
0 |
1 |
||
small project for building and indexing unitigs and simplitigs using FM-index |
last update 2024-12-17formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2024-12-17formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-12-17formatting: failedlinting: failed |
0 |
1 |
||
Materials for organization data dictionary |
last update 2024-12-17formatting: failedlinting: failed |
0 |
3 |
||
Fine mapping analysis within the pQTL pipeline project |
last update 2024-12-16formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-16formatting: passedlinting: passed |
0 |
1 |
||
No description available. |
last update 2024-12-16formatting: failedlinting: failed |
0 |
1 |
||
Single-cell PacBio and ONT data quantitation pipeline |
last update 2024-12-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-19formatting: failedlinting: failed |
0 |
3 |
||
Workflow to detect assembly and long read regions rich in GA or CT alleles. |
last update 2024-12-19formatting: failedlinting: failed |
0 |
2 |
||
Analyze single-end RNA-Seq data |
last update 2024-12-18formatting: failedlinting: failed |
0 |
3 |
||
Setting up snakemake for use on Digital Research Alliance of Canada advanced computing clusters. |
last update 2024-10-30formatting: failedlinting: failed |
0 |
1 |
||
STAR + edgeR/DESeq2/limma-voom + GSEA RNA-seq gene expression analysis workflow |
bioinformatics-analysis bioinformatics-pipeline computational-biology snakemake-workflows snakemake-pipelines bioinformatics |
last update 2024-10-30formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2024-10-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-10-26formatting: passedlinting: failed |
0 |
1 |
||
Snakemake workflow for a basic single-cell RNA-Seq analysis. |
python snakemake scanpy single-cell-rna-sequencing |
last update 2024-12-10formatting: failedlinting: failed |
0 |
1 |
|
Snakemake Pipeline for Creating an Alternate Reference Genome unique to a triploid asexual Arctic Da… |
alternate-reference-genome arctic daphnia-pulex daphnia-pulicaria snakemake triploid |
last update 2024-10-25formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2024-10-25formatting: failedlinting: failed |
0 |
1 |
||
Quick-and-dirty differential gene expression analysis pipeline that avoids computationally demanding… |
last update 2024-10-25formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2024-10-24formatting: failedlinting: failed |
0 |
1 |
||
A self contained snakemake workflow to test new features |
last update 2024-10-24formatting: failedlinting: failed |
0 |
2 |
||
K-CHOPORE is a bioinformatics pipeline. It helps researchers analyze RNA modifications and transcrip… |
last update 2024-10-24formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-10-24formatting: failedlinting: failed |
0 |
1 |
||
c-HiC analysis for Glaser et al. 2024 |
last update 2024-10-24formatting: failedlinting: failed |
0 |
1 |
||
RNA-Seq Downstream Differential Gene Expression and Gene Set Enrichment Analysis |
last update 2024-11-05formatting: failedlinting: failed |
0 |
1 |
||
This is a snakemake pepeline for Stan’s workflow |
last update 2024-10-23formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-10-23formatting: failedlinting: failed |
0 |
1 |
||
Nevada-Bioinformatics-Center/snakemake_rnaseq_salmon_workflow |
No description available. |
last update 2024-10-23formatting: failedlinting: failed |
0 |
2 |
|
Nevada-Bioinformatics-Center/Nevada-Bioinformatics-Center-snakemake_suppa_diffsplice_workflow |
No description available. |
last update 2024-10-23formatting: failedlinting: failed |
0 |
2 |
|
No description available. |
last update 2024-10-23formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-10-22formatting: failedlinting: failed |
0 |
3 |
||
Snakemake pipeline to analyze clonal evoltion in single and matched tumor samples |
last update 2024-11-08formatting: failedlinting: failed |
0 |
1 |
||
Python-based workflow for reproducible and scalable minimal processing with the HCPPipelines. |
last update 2024-11-08formatting: failedlinting: failed |
0 |
1 |
||
Workflow for processing UAS imagery into data on bird location and species for near real-time monito… |
last update 2024-11-08formatting: failedlinting: failed |
0 |
4 |
||
No description available. |
last update 2024-11-07formatting: failedlinting: failed |
0 |
1 |
||
A framework for validating variant calling methods in cancer genomics, focusing on addressing the ch… |
last update 2024-11-06formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-04formatting: failedlinting: passed |
0 |
1 |
||
Workflow module for mapping |
last update 2024-11-02formatting: failedlinting: failed |
0 |
0 |
||
Snakemake port of https://github.com/fedorrik/HumAS-HMMER_for_AnVIL/tree/main. |
last update 2024-11-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-10-31formatting: failedlinting: failed |
0 |
1 |
||
Workflow to map long reads back to an assembly. |
last update 2024-11-22formatting: passedlinting: failed |
0 |
0 |
||
No description available. |
last update 2024-11-15formatting: failedlinting: failed |
0 |
1 |
||
SnakeMake workflow to perform duplex baecall of r9.4.1 data |
last update 2024-11-14formatting: failedlinting: failed |
0 |
1 |
||
Variant effect prediction using Kipoi |
last update 2024-11-14formatting: failedlinting: failed |
0 |
1 |
||
Simple Snakemake pipeline for conducting association analysis of common variants. |
last update 2024-11-14formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-14formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-13formatting: passedlinting: failed |
0 |
1 |
||
This repository is for experimenting with/iterating on snakemake configurations for a sample project… |
last update 2024-11-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-13formatting: failedlinting: failed |
0 |
1 |
||
k-mer length analysis |
last update 2024-11-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-12formatting: failedlinting: failed |
0 |
0 |
||
Repository containing bioinformatic code for macro-scale host transcriptomic data processing |
pipeline |
last update 2024-11-12formatting: passedlinting: passed |
0 |
1 |
|
Silly functions and rules to make bigger pipelines manageable |
last update 2024-11-12formatting: passedlinting: passed |
0 |
1 |
||
Pipeline to analyze DNA sequencing data with legacy compatibility for the Pool lab’s Drosophila Geno… |
last update 2024-11-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-10formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-07-19formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-09formatting: failedlinting: failed |
0 |
2 |
||
Strain-informed gene content inference using metagenomic data |
last update 2024-11-09formatting: passedlinting: failed |
0 |
2 |
||
Workflow module for variant calling |
last update 2024-11-09formatting: failedlinting: passed |
0 |
0 |
||
No description available. |
last update 2024-11-08formatting: failedlinting: failed |
0 |
2 |
||
Pipeline for generating and updating the BGE gap list |
last update 2024-11-21formatting: failedlinting: failed |
0 |
3 |
||
miRNA-Seq analysis workflow using bowtie and DESeq2 |
last update 2024-11-20formatting: failedlinting: failed |
0 |
1 |
||
Mapping of RNAseq reads to sequences obtained from CryoEM in Toxoplasma gondii |
last update 2024-11-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-19formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake workflow for discovering novel alleles with PacBio HiFi reads |
last update 2024-11-19formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-11-19formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-18formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for MiSeq array data processing |
last update 2024-11-18formatting: failedlinting: failed |
0 |
1 |
||
Snakemake settings for Great Lakes HPC Cluster @ UM |
last update 2024-11-18formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-18formatting: failedlinting: failed |
0 |
1 |
||
ProteoSeq: A proteogenomics workflow leveraging long-read RNA-seq data for discovery of isoform-leve… |
long-read-sequencing proteogenomics proteomics rna-seq |
last update 2024-11-18formatting: failedlinting: failed |
0 |
3 |
|
A Snakemake workflow for encrypting files before uploading them to the European Genome-Phenome Archi… |
last update 2024-11-18formatting: passedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-11-18formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow to automatically quantify gene expression with Salmon using local and SRA samples |
last update 2024-11-15formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow to quantify sample coverage across a set of reference genomes/MAGs |
last update 2024-11-15formatting: failedlinting: failed |
0 |
1 |
||
MeerKAT view of Hickson Compact Groups: I. Data description and release |
last update 2024-11-15formatting: failedlinting: failed |
0 |
1 |
||
Snakemake-ified Alignment for ONT Data |
last update 2024-11-15formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-11-28formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-12-12formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-11-27formatting: failedlinting: failed |
0 |
4 |
||
No description available. |
last update 2024-11-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-27formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-11-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-27formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-11-26formatting: failedlinting: failed |
0 |
1 |
||
Applied Health Data Science 2024 |
last update 2024-11-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-25formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2024-11-25formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2024-11-25formatting: failedlinting: failed |
0 |
2 |
||
Public repository for CIDC’s WES2 pipeline releases |
last update 2024-11-25formatting: failedlinting: failed |
0 |
3 |
||
Pipeline for Somatic Variant Calling with WES and WGS data |
last update 2024-11-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-23formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-22formatting: failedlinting: failed |
0 |
1 |
||
repeats single-cell RNA-seq |
last update 2024-11-22formatting: failedlinting: failed |
0 |
1 |
||
FUSILLI: Fusion Utility for Scanning and Identification of Library Linked Interactions |
last update 2024-11-22formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-04formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-12-04formatting: passedlinting: failed |
0 |
1 |
||
Code for mGWAS with H. influenzae |
last update 2024-12-04formatting: failedlinting: failed |
0 |
1 |
||
Code for data processing, statistical models, and figure generation for Variance partitioning in Eco… |
last update 2024-12-04formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-03formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for detection limit test |
pipeline |
last update 2024-12-03formatting: passedlinting: failed |
0 |
1 |
|
snakemake workflow for RNA-Seq data analysis using bowtie |
last update 2024-12-03formatting: passedlinting: passed |
0 |
1 |
||
Bacterial Genome Assembly & Annotation Pipeline |
last update 2024-12-03formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2024-12-02formatting: failedlinting: failed |
0 |
0 |
||
Snakemake pipeline for processing ChIP-seq and ATAC-seq data |
last update 2024-12-02formatting: failedlinting: failed |
0 |
1 |
||
Snakemake-GenomePipeline is a scalable and reproducible workflow for genome analysis using the Snake… |
last update 2024-12-02formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow to analyse hematological malignancies in whole genome data |
last update 2024-12-11formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-12-02formatting: failedlinting: failed |
0 |
1 |
||
This is the repository for my AHDS final project. |
last update 2024-12-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-02formatting: failedlinting: failed |
0 |
1 |
||
Proof of concept for SV genotyper using Novoalign MAPQ |
last update 2024-12-01formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-29formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-11-29formatting: failedlinting: failed |
0 |
1 |
||
Codebase exploring figure-ground segregation in texture stimuli through neural synchrony mechanisms…. |
last update 2024-11-29formatting: failedlinting: failed |
0 |
1 |
||
Snakemake Pipeline for Bacteria |
last update 2024-11-29formatting: failedlinting: failed |
0 |
1 |
||
Align almost any kind of RNA-seq data |
last update 2024-12-10formatting: passedlinting: passed |
0 |
1 |
||
No description available. |
last update 2024-12-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-09formatting: failedlinting: failed |
0 |
1 |
||
Accompanying Repository for ‘Random Abstract Cell Complexes’ Paper. |
last update 2024-12-09formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-12-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-08formatting: failedlinting: failed |
0 |
1 |
||
gene phylogenetic species check with uniprotKB database |
last update 2024-12-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-18formatting: failedlinting: failed |
0 |
1 |
||
DE analysis of ribo-seq datasets |
last update 2024-12-18formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-12-12formatting: failedlinting: failed |
0 |
1 |
||
Pranavi-Hiba-Saby |
last update 2024-12-12formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-12-12formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-12-11formatting: failedlinting: failed |
0 |
1 |
||
A repository for efficient population genomic analysis using Snakemake workflow. |
genome-analysis ngs ngs-analysis population population-genomics snakemake-workflow variant-calling whole rprogramming |
last update 2024-12-11formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2024-12-11formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-12-11formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-12-11formatting: failedlinting: failed |
0 |
0 |
||
Convert plink files to hdf5 |
last update 2024-12-11formatting: failedlinting: failed |
0 |
1 |
||
Final Project |
last update 2024-12-11formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-12-10formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2024-12-10formatting: failedlinting: failed |
0 |
1 |
||
Basic bioinformatics pipeline (Snakemake) to annotate VCF files with ANNOVAR |
bioinformatics docker flask github pipeline snakemake vcf |
last update 2024-12-10formatting: failedlinting: failed |
0 |
1 |
|
Snakemake workflow to generate BAM alignment statistics on the BIH cluster. |
bam hg38 mm10 quality-control t2t snakemake sequencing |
last update 2024-12-10formatting: failedlinting: failed |
0 |
0 |
|
A snakemake workflow to produce mode-resolved INS intensities in incoherent approximation |
last update 2024-08-23formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-08-23formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2024-08-23formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-08-23formatting: failedlinting: failed |
0 |
2 |
||
Wrapper for BLASSO-for-Rhodopsins |
last update 2024-08-22formatting: failedlinting: failed |
0 |
4 |
||
Snakemake workflow for mining Marchantia polymorpha DNA sequences for viruses. |
last update 2024-08-22formatting: failedlinting: passed |
0 |
1 |
||
Snakemake workflow for bulk RNA sequencing with pytximport. |
last update 2024-08-22formatting: passedlinting: failed |
0 |
1 |
||
Analysis of a multi-mutant, barcoded influenza H3 library in the A/HongKong/45/2019 background. |
last update 2024-08-20formatting: failedlinting: failed |
0 |
4 |
||
No description available. |
last update 2024-08-20formatting: failedlinting: failed |
0 |
1 |
||
Repository to generate the input data files used for the MEIHAWAI model |
last update 2024-08-18formatting: failedlinting: failed |
0 |
0 |
||
Overview of IMAP - Integrated Microbiome Analysis Pipelines |
last update 2024-08-17formatting: failedlinting: failed |
0 |
1 |
||
Lightweight snakemake pipeline for preprocessing, alignmen, and QC of PROseq/ChROseq data |
last update 2024-08-29formatting: failedlinting: failed |
0 |
1 |
||
Media Mix Modelling: Lecture 3 of Digital and Social Media Strategies (DSMS) at Tilburg U |
last update 2024-08-29formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2024-08-29formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-08-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-08-28formatting: failedlinting: failed |
0 |
1 |
||
Seabreeze: an automated pipeline for structrual variant analysis of bacterial resequencing experimen… |
last update 2024-08-28formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for Whole Genome analysis with minION |
last update 2024-08-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-08-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-08-28formatting: failedlinting: failed |
0 |
1 |
||
Workflow for massive analysis of internet images |
last update 2024-08-28formatting: failedlinting: failed |
0 |
2 |
||
Dataprocessing project for converting the FAST-GBS pipeline to a snakemake pipeline. |
last update 2024-08-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-08-27formatting: failedlinting: failed |
0 |
1 |
||
Repository for my Advanced dataprocessing school project. A pipeline made with snakemake |
last update 2024-08-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-08-27formatting: passedlinting: failed |
0 |
1 |
||
Lecture on Advertising Attribution Models for Digital and Social Media Strategies at Tilburg U |
last update 2024-08-27formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2024-08-27formatting: failedlinting: failed |
0 |
1 |
||
🧬🔍CNV analysis and outcome prediction in Ultra-High-Risk and First Episode Psychosis individuals 🩺🧠 |
cnv cnv-analysis outcome-prediction psychosis wgs |
last update 2024-09-08formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2024-08-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-08-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-08-24formatting: passedlinting: failed |
0 |
1 |
||
example snakemake workflow for the 2024 SAGC workflow workshop |
last update 2024-08-24formatting: failedlinting: failed |
0 |
1 |
||
reproducibly estimate parameters for VerifyBamID2 for a new reference genome |
last update 2024-09-09formatting: passedlinting: failed |
0 |
1 |
||
Snakemake pipeline for variant annotation with VEP |
last update 2024-09-04formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-09-04formatting: failedlinting: failed |
0 |
1 |
||
2023-2024 data-process pipeline-conversion project; Adapting havoc to utilise snakemake. |
last update 2024-09-04formatting: failedlinting: failed |
0 |
1 |
||
In this repository all the codes to run the master’s thesis is hosted |
last update 2024-09-03formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-09-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-09-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-09-01formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-09-13formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-09-13formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow to re-batch POD5 files by pore/channel |
last update 2024-09-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-09-12formatting: failedlinting: failed |
0 |
1 |
||
Barcode Recovery and Comparison from Database |
last update 2024-09-12formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2024-09-11formatting: failedlinting: failed |
0 |
2 |
||
Mu-seq Workflow Utility |
last update 2024-09-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-09-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-09-09formatting: failedlinting: failed |
0 |
1 |
||
Dockerized RNA-seq analysis pipeline built with Snakemake through steps like quality control, trimmi… |
last update 2024-09-07formatting: failedlinting: failed |
0 |
1 |
||
A snakemake workflow that assemble diploid genome using HiFi and HiC sequencing reads |
last update 2024-09-07formatting: failedlinting: failed |
0 |
2 |
||
A Snakemake workflow for using SLEAP and NAPS |
behavior pose snakemake |
last update 2024-09-07formatting: passedlinting: failed |
0 |
1 |
|
No description available. |
last update 2024-09-06formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for parsing simulation outputs across scaling factors |
last update 2024-09-18formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-09-18formatting: failedlinting: failed |
0 |
1 |
||
Test data for the trip-wire workflow |
last update 2024-09-18formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake pipeline to assemble Nanopore WGS data |
last update 2024-09-18formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-09-18formatting: failedlinting: failed |
0 |
0 |
||
Field Experiments I: A/B tests - Lecture 4 of Digital and Social Media Strategies at Tilburg U |
last update 2024-09-18formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2024-09-17formatting: failedlinting: failed |
0 |
1 |
||
Counting the SNPs of specific genes related to AD in many individuals starting from raw illumina seq… |
last update 2024-09-17formatting: failedlinting: failed |
0 |
1 |
||
The repository contains scripts for wheat genome assembly of PacBio CCS reads. |
last update 2024-09-16formatting: failedlinting: failed |
0 |
1 |
||
mlops course tasks from ods community |
last update 2024-09-16formatting: failedlinting: failed |
0 |
1 |
||
Perturb-Seq Pipeline with Snakemake and Cell Ranger |
last update 2024-09-15formatting: failedlinting: failed |
0 |
1 |
||
A repository to hold the workflow for running solutionAnalysis |
last update 2024-09-14formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-09-21formatting: failedlinting: failed |
0 |
0 |
||
Workflow module for read processing |
last update 2024-09-21formatting: failedlinting: passed |
0 |
0 |
||
construct pangenome from unaligned reads |
last update 2024-09-20formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-09-19formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for QC and processing of HIC data. Results in on .cool file and TAD calls for the… |
last update 2024-09-19formatting: failedlinting: failed |
0 |
1 |
||
An awesome quantitative genetics pipeline |
last update 2024-09-19formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-09-19formatting: failedlinting: failed |
0 |
1 |
||
This repository contains a bioinformatics pipeline for annotating genetic variants from VCF files us… |
last update 2024-09-18formatting: failedlinting: passed |
0 |
1 |
||
This repository contains a Snakemake pipeline for automating genomic data analysis, with instruction… |
last update 2024-09-24formatting: failedlinting: failed |
0 |
1 |
||
A workflow to process single-cell readout of CRISPR screen performed on BD Rhapsody system |
last update 2024-09-23formatting: failedlinting: failed |
0 |
1 |
||
Performs analysis of mass spectrometry data for John Belisle’s lab. |
last update 2024-09-23formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-09-23formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2024-09-23formatting: failedlinting: failed |
0 |
0 |
||
Measure distances between two types of markers during FISH Assay after Chromosomal Translocation eve… |
bioimage-analysis cellprofiler-pipeline distance-calculation napari-visualization snakemake-workflow workflow-automation |
last update 2024-09-23formatting: failedlinting: failed |
0 |
2 |
|
No description available. |
last update 2024-09-23formatting: failedlinting: failed |
0 |
1 |
||
My PhD thesis at the University of Zurich. It contains the three papers making up the thesis, as wel… |
last update 2024-09-22formatting: failedlinting: failed |
0 |
1 |
||
Analysing options for Ukraine’s future energy supply. |
last update 2024-07-25formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-07-24formatting: failedlinting: failed |
0 |
3 |
||
This repository includes the workflow for the main experiments in the Movi paper. |
last update 2024-07-24formatting: failedlinting: failed |
0 |
1 |
||
Peak-calling using Snakemake |
last update 2024-07-24formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-07-23formatting: failedlinting: failed |
0 |
1 |
||
Analysis NGS data from P53 ampicon-based assay |
last update 2024-07-22formatting: failedlinting: failed |
0 |
1 |
||
Methylation tools repository |
last update 2024-07-19formatting: failedlinting: failed |
0 |
1 |
||
Peptigate (peptide + investigate) predicts bioactive peptides from transcriptome assemblies or sets … |
last update 2024-07-18formatting: passedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-07-17formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-07-17formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-07-17formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-07-17formatting: passedlinting: failed |
0 |
1 |
||
Build genome references for RENEE |
last update 2024-08-06formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2024-08-06formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-08-05formatting: failedlinting: failed |
0 |
0 |
||
Repository for varroa linkage mapping project |
last update 2024-08-04formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-08-03formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-08-02formatting: passedlinting: failed |
0 |
1 |
||
Code associated with Onset of infectiousness explains differences in transmissibility across Mycobac… |
last update 2024-08-02formatting: failedlinting: failed |
0 |
1 |
||
Hnld_Genetic_Diversity_Analysis |
last update 2024-08-02formatting: failedlinting: failed |
0 |
1 |
||
Generate single-cell reference dataset for deconvolution in Atlas |
last update 2024-08-02formatting: failedlinting: failed |
0 |
5 |
||
No description available. |
last update 2024-08-02formatting: failedlinting: failed |
0 |
1 |
||
Lecture 1 of DSMS: Course Introduction |
last update 2024-08-01formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2024-08-01formatting: failedlinting: failed |
0 |
2 |
||
A Snakemake workflow for Chandra data reduction |
chandra ciao data-reduction snakemake pylira |
last update 2024-07-30formatting: failedlinting: failed |
0 |
3 |
|
No description available. |
last update 2024-07-25formatting: failedlinting: failed |
0 |
1 |
||
PacBio Jasmine pipeline, penalized regression, and DMR identification |
last update 2024-08-13formatting: failedlinting: failed |
0 |
1 |
||
Deep mutational scanning of the MERS-CoV and PDF-2180 receptor-binding domains |
last update 2024-08-13formatting: failedlinting: failed |
0 |
0 |
||
WIP HIBF benchmarks |
last update 2024-08-13formatting: passedlinting: failed |
0 |
6 |
||
Remove and Quantify Organism Spike Reads from Sequencing Data |
last update 2024-08-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-08-11formatting: passedlinting: failed |
0 |
1 |
||
next step after recount-pump in the monorail pipeline |
last update 2024-08-09formatting: failedlinting: failed |
0 |
5 |
||
No description available. |
last update 2024-08-09formatting: failedlinting: failed |
0 |
3 |
||
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopor… |
bacterial-genome-analysis bioinformatics-pipeline nanopore-sequencing snakemake |
last update 2024-08-14formatting: passedlinting: passed |
0 |
1 |
|
Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing us… |
bacterial-genome-analysis bioinformatics bioinformatics-pipeline nanopore-sequencing snakemake snakemake-workflow |
last update 2024-08-14formatting: passedlinting: failed |
0 |
1 |
|
A snakemake-based workflow for converting Illumina’s bcl files to fastq files with the option of fur… |
last update 2024-08-08formatting: failedlinting: failed |
0 |
1 |
||
Multiplex Accurate Sensitive Quantitation (MASQ) analysis and primer design |
last update 2024-08-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-08-07formatting: failedlinting: failed |
0 |
1 |
||
Bash script and basic structure to install and run a snakemake workflow |
last update 2024-08-16formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-08-15formatting: failedlinting: failed |
0 |
1 |
||
Workspace for adding DFTs to Psi4 and testing them against ACCDB |
last update 2024-08-15formatting: failedlinting: failed |
0 |
0 |
||
ss |
last update 2024-07-16formatting: failedlinting: failed |
0 |
1 |
||
Robust reproducible differential expression analysis based on edgeR with components in R and Python … |
last update 2024-07-16formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2024-07-14formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-07-13formatting: failedlinting: failed |
0 |
3 |
||
https://agc.readthedocs.io/ on REANA |
last update 2024-07-13formatting: failedlinting: failed |
0 |
5 |
||
An app that removes empty images from camera trap datasets using MD. Comes with a simple GUI. |
last update 2024-07-12formatting: failedlinting: failed |
0 |
1 |
||
Predict variant calling performance across the genome |
last update 2024-07-11formatting: failedlinting: failed |
0 |
0 |
||
Genome-in-a-Bottle stratifications for major references |
last update 2024-07-11formatting: passedlinting: failed |
0 |
0 |
||
A pipeline for quantification of antibody staining in TMA cores. |
last update 2024-07-11formatting: failedlinting: failed |
0 |
1 |
||
Example repository for analyzing many datasets at once from scperturb.org using snakemake |
perturbation-methods single-cell transcriptomics |
last update 2024-07-21formatting: failedlinting: failed |
0 |
1 |
|
deep_snake - snakemake-based deepconsensus (Pacbio SequelII subreads - to deepconsensus.fastq) |
last update 2024-07-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-07-11formatting: failedlinting: failed |
0 |
2 |
||
Snakemake workflow: DNA Single Nucleotide Variant Calling |
last update 2024-07-10formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-07-10formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-07-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-07-08formatting: failedlinting: failed |
0 |
1 |
||
STROMBOLI is a snakemake pipeline for associating barcodes with genetic variants using long-read seq… |
last update 2024-07-08formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-07-16formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-09-11formatting: failedlinting: failed |
0 |
0 |
||
Cross validation workflow of Semi-binary Matrix Factorization (SBMF) |
last update 2024-07-05formatting: failedlinting: failed |
0 |
1 |
||
Cross validation workflow of Semi-Binary Symmetric Matrix Tri-Factorization (SBSMTF) |
last update 2024-07-05formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-07-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-07-04formatting: failedlinting: failed |
0 |
4 |
||
No description available. |
last update 2024-07-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-07-03formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-07-03formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-07-02formatting: failedlinting: failed |
0 |
1 |
||
[WIP] Automatic dataflow for HADES data |
last update 2024-07-02formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-07-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-07-02formatting: failedlinting: failed |
0 |
3 |
||
Snakemake Pipeline to Calculate iKIR Score from SNP Imputations or scRNA-Seq Typing |
last update 2024-07-02formatting: failedlinting: failed |
0 |
1 |
||
For demultiplexing and creating consensus from Indexed PacBio reads from SGA PCR. |
last update 2024-07-01formatting: failedlinting: failed |
0 |
4 |
||
Genome analysis experiments using StratoMod pipeline |
last update 2024-07-01formatting: passedlinting: failed |
0 |
0 |
||
No description available. |
last update 2024-07-01formatting: passedlinting: passed |
0 |
1 |
||
No description available. |
last update 2024-07-01formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-06-30formatting: failedlinting: failed |
0 |
1 |
||
A snakemake pipeline to KIR-HLA genotype 10X Genomics Results |
last update 2024-06-30formatting: failedlinting: failed |
0 |
1 |
||
This is for the review paper about Ancestral Recombination Graph by Nielsen lab |
last update 2024-06-29formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-06-29formatting: passedlinting: passed |
0 |
1 |
||
An example Snakemake project for Aalto Triton. |
last update 2024-08-02formatting: failedlinting: passed |
0 |
6 |
||
snakemake, singularity, pyBIS based RNAseq workflow to be executed on the ETH Zurich LeoMed Slurm Cl… |
python |
last update 2024-06-27formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2024-06-26formatting: failedlinting: failed |
0 |
1 |
||
A minimal proof-of-concept workflow for Latch’s native Snakemake support |
last update 2024-06-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-06-25formatting: failedlinting: failed |
0 |
1 |
||
Thema 11 subject Dataproccesing |
last update 2024-06-24formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-06-23formatting: failedlinting: failed |
0 |
1 |
||
Workflow para anotação de variantes |
last update 2024-06-22formatting: failedlinting: failed |
0 |
1 |
||
First module of the gnomAD-SV pipeline |
last update 2024-06-21formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-06-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-06-20formatting: failedlinting: failed |
0 |
1 |
||
Longevity of Artifacts in Leading Parallel and Distributed Systems Conferences: a Review of the Stat… |
last update 2024-06-20formatting: failedlinting: failed |
0 |
5 |
||
No description available. |
last update 2024-06-19formatting: failedlinting: failed |
0 |
1 |
||
Workflow module for assembly |
last update 2024-06-19formatting: failedlinting: failed |
0 |
0 |
||
Contains the papers The Value of Being Indispensable, Hybrid platforms and bargaining power and rela… |
last update 2024-08-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-08-21formatting: failedlinting: failed |
0 |
4 |
||
A workflow for predicting ligands and protein interactions with NeuralPlexer |
last update 2024-06-18formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-06-17formatting: failedlinting: failed |
0 |
1 |
||
a repository for evaluating drug repositioning methods. |
last update 2024-06-16formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2024-06-15formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-06-14formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2024-06-14formatting: failedlinting: failed |
0 |
1 |
||
Shiny GUI with Snakemake backbone to perform modular ONT Data Analysis Pipelines |
last update 2024-06-13formatting: failedlinting: failed |
0 |
1 |
||
Repo to exemplify issue when importing Python modules within Snakemake modules |
last update 2024-06-12formatting: failedlinting: failed |
0 |
1 |
||
Complete workflow for primary data analyses for bacterial genomes using nanopore |
last update 2024-06-12formatting: failedlinting: failed |
0 |
1 |
||
Complete workflow for primary data analyses for bacterial genomes using Illumina |
last update 2024-06-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-08-08formatting: failedlinting: failed |
0 |
1 |
||
Complete workflow for quality controle of assemblies form bacterial genomes. |
last update 2024-06-12formatting: failedlinting: failed |
0 |
1 |
||
Annual probability of extreme heat and drought events, derived from Lange et al 2020 |
last update 2024-06-11formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-06-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-06-10formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-06-10formatting: failedlinting: failed |
0 |
1 |
||
Pipeline for SLU Lepidium campestre GWAS project |
last update 2024-06-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-06-08formatting: failedlinting: failed |
0 |
1 |
||
Code to get the encode datasets that will get run through ABC + Encode-rE2G |
last update 2024-06-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-06-07formatting: failedlinting: failed |
0 |
1 |
||
Analysing the preferences of people about policy instruments targeting the building and transport se… |
last update 2024-06-07formatting: failedlinting: failed |
0 |
1 |
||
A basic and straightforward ancient DNA data preprocessing pipeline. Mainly designed for genetic rel… |
last update 2024-07-26formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake workflow to produce accessible datasets for PMC publication metadata |
last update 2024-06-06formatting: failedlinting: failed |
0 |
1 |
||
BIH |
last update 2024-06-29formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-06-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-06-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-06-04formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2024-06-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-06-04formatting: failedlinting: failed |
0 |
1 |
||
Find and quantify pathogens with kraken2 and bowtie2 as in Lu et al 2022 |
last update 2024-06-04formatting: passedlinting: failed |
0 |
1 |
||
Twist Cancer hydragenetics pipeline for HG38 |
last update 2024-06-04formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2024-06-03formatting: failedlinting: failed |
0 |
1 |
||
Perform Split K-mer Analysis to identify sample species (based on k-mers in NGS reads). |
last update 2024-06-03formatting: passedlinting: failed |
0 |
1 |
||
Workflow for virus detection in metagenomic data from project PHEW |
last update 2024-06-03formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2024-06-03formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for orchestration of the LEGEND simulation chain |
legend simulations snakemake |
last update 2024-06-01formatting: failedlinting: failed |
0 |
2 |
|
snakemake workflow to reproduce the figures of the article MethNet: a robust approach to identify re… |
last update 2024-05-31formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow to profile the MLST of known bacteria in metagenomic data |
last update 2024-05-31formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake pipeline for drug-resistance profiling using HIV whole-genome NGS data |
last update 2024-06-07formatting: failedlinting: failed |
0 |
0 |
||
Snakemake workflow for single-cell ATAC data |
last update 2024-05-29formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for the automatic generation of GRN’s from SRR accessions |
last update 2024-05-28formatting: failedlinting: failed |
0 |
1 |
||
variant effect predictions |
last update 2024-05-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-05-27formatting: failedlinting: failed |
0 |
1 |
||
Blokadniki |
last update 2024-05-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-05-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-05-25formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-05-24formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-05-24formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-05-30formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-05-23formatting: failedlinting: passed |
0 |
1 |
||
Compare sequencing runs and genomes with sourmash, skmer and sylph sketches |
last update 2024-05-22formatting: passedlinting: failed |
0 |
1 |
||
From an Mtb genome’s SRA accession number, fetch and process paired-read sequencing data for lineage… |
last update 2024-05-21formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-05-21formatting: failedlinting: failed |
0 |
2 |
||
Downloading fastq reads from SRA database |
last update 2024-05-19formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-05-17formatting: failedlinting: failed |
0 |
1 |
||
playing with Snakemake include keyword |
last update 2024-05-16formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-05-16formatting: failedlinting: failed |
0 |
1 |
||
Population-based framework for introgression/selection/resequencing experiments |
last update 2024-05-15formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-05-15formatting: failedlinting: failed |
0 |
1 |
||
Scripts and full pipeline for the nioz internship |
last update 2024-05-15formatting: failedlinting: failed |
0 |
1 |
||
A workflow made with snakemake to analyse differential gene expression. |
last update 2024-05-14formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2024-05-14formatting: passedlinting: passed |
0 |
2 |
||
pipeline for variant calling, DNM filtering, and annotating WGS data |
last update 2024-05-13formatting: failedlinting: failed |
0 |
1 |
||
Work in progress converting epigenome-wide association analysis pipeline into a reproducible snakema… |
last update 2024-05-13formatting: failedlinting: failed |
0 |
0 |
||
Long read transcriptome pipeline for Pacbio and ONT |
last update 2024-05-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-05-13formatting: failedlinting: failed |
0 |
1 |
||
Variant calling |
last update 2024-05-12formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2024-05-10formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2024-05-10formatting: failedlinting: failed |
0 |
1 |
||
repository for con-gen-csu class project |
last update 2024-05-10formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-05-10formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2024-05-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-06-21formatting: failedlinting: failed |
0 |
1 |
||
Preprocessing microbiome fastq reads using Seqkit, FastQC, MultiQC, bbmap, etc. |
last update 2024-05-08formatting: failedlinting: failed |
0 |
1 |
||
Microbiome data cleaning, tidying and transformation |
last update 2024-05-08formatting: failedlinting: failed |
0 |
1 |
||
I am building a bioinformatics pipeline with python, R and snakemake |
last update 2024-05-08formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-05-08formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
snakemake-workflow genome-assembly loxodes internal-eliminated-sequences |
last update 2024-05-06formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2024-05-06formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-05-06formatting: passedlinting: passed |
0 |
1 |
||
Final project for CS50. |
last update 2024-05-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-05-05formatting: failedlinting: failed |
0 |
1 |
||
Predictive modeling for microbiome data |
last update 2024-05-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-05-03formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-05-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-05-02formatting: failedlinting: failed |
0 |
3 |
||
A research repository for creating a linked data dataset for Syriac manuscript descriptions |
last update 2024-05-01formatting: failedlinting: failed |
0 |
1 |
||
Fastq QC pipeline for fast project delivery, also called nopipe. |
last update 2024-05-01formatting: failedlinting: failed |
0 |
1 |
||
Code used for to develop the manuscript: Cortical Network Disruption is Minimal in Early Stages of P… |
last update 2024-05-01formatting: failedlinting: failed |
0 |
1 |
||
Mini Snakemake pipeline rendering a quarto report |
last update 2024-04-30formatting: failedlinting: passed |
0 |
2 |
||
A Snakemake workflow to produce accessible datasets for ArXiv publication metadata |
last update 2024-06-06formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for assembly |
last update 2024-04-30formatting: failedlinting: failed |
0 |
1 |
||
Snakemake nedir ve çalışma prensipleri nelerdir ? |
last update 2024-04-29formatting: failedlinting: failed |
0 |
1 |
||
long read differential expression analysis |
last update 2024-06-28formatting: passedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-06-28formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-04-29formatting: failedlinting: failed |
0 |
1 |
||
Pipeline that detects defence systems in bacterial genome sequences. |
last update 2024-04-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-04-28formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-04-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-04-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-04-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-04-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-04-26formatting: failedlinting: failed |
0 |
1 |
||
pipeline for post-transcriptional regulation analysis- m6A, polyA tail, and isoform - with nanopore … |
last update 2024-04-26formatting: failedlinting: failed |
0 |
1 |
||
Exploring the microbiome analysis output |
last update 2024-04-25formatting: failedlinting: failed |
0 |
1 |
||
Microbiome data analysis using Mothur platform |
last update 2024-04-25formatting: failedlinting: failed |
0 |
1 |
||
Exploring microbiome sample metadata |
last update 2024-04-25formatting: failedlinting: failed |
0 |
1 |
||
Essential software for microbiome data analysis |
last update 2024-04-25formatting: failedlinting: failed |
0 |
1 |
||
temp |
last update 2024-04-25formatting: failedlinting: failed |
0 |
0 |
||
Workflow for processing targeted AR gene panel sequencing data |
last update 2024-04-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-04-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-04-25formatting: failedlinting: passed |
0 |
0 |
||
No description available. |
last update 2024-04-24formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2024-04-24formatting: failedlinting: passed |
0 |
1 |
||
Snakemake pipeline for running EMU |
last update 2024-04-23formatting: failedlinting: passed |
0 |
0 |
||
No description available. |
last update 2024-04-22formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-04-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-04-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-04-21formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-04-21formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-04-19formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2024-04-19formatting: failedlinting: failed |
0 |
1 |
||
CRISPRkat |
last update 2024-04-19formatting: failedlinting: failed |
0 |
1 |
||
DNA2A (DNA (A)ssembly and (A)nalyzer) is a comprehensive toolkit for the automated analysis of eukar… |
last update 2024-04-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-02-05formatting: failedlinting: failed |
0 |
1 |
||
Code for analysing the molecular and phenotypic data obtained during the TRANSLATE NAMSE project |
last update 2023-02-10formatting: failedlinting: failed |
0 |
3 |
||
Snakemake workflow for quantifying transcript expression using Salmon (QuteS) in the mapping-based m… |
last update 2023-11-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-06-13formatting: failedlinting: failed |
0 |
2 |
||
Snakemake port of WGDdetector, a pipeline to detect Whole Genome Duplications (Yang et al 2019) |
last update 2024-04-15formatting: passedlinting: passed |
0 |
1 |
||
No description available. |
last update 2024-03-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-02-29formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow to download and process public metagenomic sequence datasets |
last update 2024-04-11formatting: failedlinting: failed |
0 |
1 |
||
Public repo for upcoming killifish paper |
last update 2023-11-22formatting: failedlinting: failed |
0 |
1 |
||
DNA methylation analysis for EPIC-CD vedolizumab and ustekinumab |
last update 2024-04-12formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow using FDA-ARGOS benchmarking dataset to compare QC metrics from short-read assemb… |
last update 2024-04-10formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-02-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-04-10formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-04-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-04-05formatting: failedlinting: failed |
0 |
1 |
||
Workflow for RNA purification sequence analysis |
last update 2024-04-08formatting: failedlinting: failed |
0 |
1 |
||
Differential gene expression analysis for samples with replicates using STAR-DeSeq2 pipeline |
deseq2-analysis rna rna-seq-analysis rna-seq-pipeline snakemake-workflow star-aligner differential-gene-expression |
last update 2024-02-11formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2024-04-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-04-10formatting: failedlinting: failed |
0 |
1 |
||
A paper about quasiseparable matrices for GPs |
last update 2024-04-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-07-12formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2024-03-21formatting: failedlinting: failed |
0 |
0 |
||
Minimally Viable UBS-seq Pipline |
last update 2024-04-02formatting: failedlinting: failed |
0 |
1 |
||
snakemake based RNAseq workflow to be executed on the ETH Zurich Euler Cluster |
last update 2024-04-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-04-02formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2024-04-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-04-01formatting: failedlinting: failed |
0 |
1 |
||
Automated maximum likelihood (ML) phylogenetic analysis using RAxML-NG and the associated tools. Pro… |
last update 2024-04-01formatting: failedlinting: failed |
0 |
1 |
||
Use specific sourmash index to quantify bacterial taxa from metagenomic samples |
last update 2023-08-15formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-03-28formatting: failedlinting: failed |
0 |
1 |
||
Example of a workflow for resilient download of data |
last update 2024-03-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-03-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-03-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-03-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
bioinformatics snakemake genomics rna-seq-analysis |
last update 2024-03-22formatting: failedlinting: failed |
0 |
4 |
|
No description available. |
last update 2024-05-17formatting: failedlinting: failed |
0 |
1 |
||
Animal-and-Food-Genomics-Group/comprehensive-atlas-of-numts-pig |
No description available. |
last update 2024-03-21formatting: failedlinting: failed |
0 |
0 |
|
Repository including workflow and scripts for A comprehensive atlas of nuclear sequences of mitochon… |
last update 2024-03-21formatting: failedlinting: failed |
0 |
1 |
||
Better wavelength calibration for Hector |
last update 2024-03-21formatting: passedlinting: failed |
0 |
1 |
||
Snakebatch pre-processing for LOBE study |
last update 2024-03-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-03-01formatting: failedlinting: failed |
0 |
1 |
||
An awesome Hi-C + ChIP (HiChIP) sequencing pipeline. |
chip-seq hi-c hichip pipeline singularity snakemake |
last update 2024-01-19formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2024-03-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-05-20formatting: failedlinting: failed |
0 |
0 |
||
Pipeline to get the genomic organization, box type and host gene biotype of snoRNAs across various e… |
last update 2024-02-29formatting: failedlinting: failed |
0 |
1 |
||
Implementation accompanying the multicompartment diffusion-chapter in the second volume of the mri2f… |
last update 2024-03-15formatting: failedlinting: failed |
0 |
2 |
||
Analysis of predictive value of escape scores from Welsh et al. 2023 experimental data |
last update 2024-03-09formatting: failedlinting: failed |
0 |
2 |
||
deep mutational scanning of the porcine deltacoronavirus receptor-binding domain |
last update 2023-03-13formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2024-03-13formatting: passedlinting: passed |
0 |
1 |
||
No description available. |
last update 2024-01-04formatting: failedlinting: failed |
0 |
2 |
||
RNA-seq pipeline for Mustafa’s paper |
last update 2022-05-12formatting: failedlinting: failed |
0 |
0 |
||
Files pertaining to the bulk RNA sequencing pipeline used by the Olive Research Group at Michigan St… |
last update 2024-03-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-06-29formatting: failedlinting: failed |
0 |
1 |
||
backup of repo initially present on gitlab.inria.fr |
last update 2024-03-11formatting: failedlinting: failed |
0 |
1 |
||
A Pipeline for General Population-Wide Analyses in Bacteria |
last update 2024-03-10formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for running multiple methdemons in a cluster environment |
last update 2024-02-07formatting: failedlinting: failed |
0 |
1 |
||
Benchmarking TE quantification from bulk RNA-seq data |
last update 2023-11-09formatting: passedlinting: failed |
0 |
2 |
||
JacquelinLai/Exploring-Wine-Quality-through-Advanced-Data-Techniques |
No description available. |
last update 2024-03-07formatting: failedlinting: failed |
0 |
1 |
|
The Mystery of Parasites |
last update 2024-03-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-04-16formatting: passedlinting: passed |
0 |
1 |
||
This is a pipeline for exploring viruses (ssDNA, dsDNA phage, and giant DNA viruses) and viral diver… |
bioinformatics-pipeline snakemake-workflow viral-metagenomics |
last update 2023-11-16formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2024-02-28formatting: failedlinting: failed |
0 |
1 |
||
Costerton Biofilm Center RNA-sequencing analysis pipeline |
last update 2024-02-19formatting: failedlinting: failed |
0 |
1 |
||
Manuscript and data describing joint visualization of influenza serology and phylogeny |
last update 2023-03-07formatting: failedlinting: failed |
0 |
8 |
||
No description available. |
last update 2024-02-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-05-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-03-04formatting: failedlinting: failed |
0 |
1 |
||
MBB 2022 K BDAP |
last update 2023-12-12formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-02-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-02-29formatting: failedlinting: failed |
0 |
1 |
||
ngs pipeline for childhood cancer data |
last update 2024-02-29formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-02-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-02-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-02-28formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2023-05-04formatting: failedlinting: failed |
0 |
2 |
||
CC_vel takes in single cell RNAseq data, establishes a cell cycle based pseudotime and calculates th… |
last update 2023-11-10formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for single-cell RNA-seq analysis |
last update 2023-07-22formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-02-27formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-02-26formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for new experiments processing, reprocessing and recalculations steps |
last update 2023-05-15formatting: failedlinting: failed |
0 |
5 |
||
No description available. |
last update 2024-02-23formatting: failedlinting: passed |
0 |
1 |
||
Snakemake pipeline for Epicure analyses |
last update 2024-02-23formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for de novo ddRAD analysis of Rana pretiosa with demultiplexed fastqs |
last update 2024-05-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-06-23formatting: failedlinting: failed |
0 |
1 |
||
Atlas analysis for controlled-access GTEx bulk datasets |
gtex rna-seq |
last update 2023-04-06formatting: failedlinting: passed |
0 |
5 |
|
Protocol to identify shared transcriptional risks between diseases and compounds predicted to result… |
last update 2024-02-19formatting: passedlinting: failed |
0 |
1 |
||
A Snakemake powered pipeline developed to perform variant-effect-prediction and frequency analysis g… |
pharmacogenetics pipeline snakemake |
last update 2023-07-18formatting: failedlinting: failed |
0 |
3 |
|
No description available. |
last update 2024-02-14formatting: failedlinting: failed |
0 |
1 |
||
Microbial Pangenome Interpretation |
last update 2024-02-14formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake workflow to basecall, quality control and assemble Nanopore data. |
last update 2022-11-02formatting: failedlinting: failed |
0 |
1 |
||
Cut&Run pipeline used in Vega-Sendino, Olbrich et al. |
last update 2024-02-14formatting: failedlinting: failed |
0 |
1 |
||
Comparison of Jolideco against other deconvolution methods. |
last update 2024-02-13formatting: failedlinting: failed |
0 |
1 |
||
troubleshooting containerization of Snakemake workflow with a global conda directive |
last update 2024-02-12formatting: failedlinting: failed |
0 |
1 |
||
Mobile Element Locator Tool (MELT) as a Snakemake workflow. |
last update 2024-02-11formatting: failedlinting: failed |
0 |
1 |
||
Workflow for differential gene expression analysis for non-replicate samples using DEGseq |
differential-gene-expression rna-seq-analysis rna-seq-pipeline snakemake-workflow star-aligner |
last update 2024-02-11formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2022-02-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-02-08formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for functional annotation using eggNOG mapper v2 |
last update 2023-05-24formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for variant identification from RNAseq data |
last update 2023-12-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-04-28formatting: failedlinting: failed |
0 |
5 |
||
No description available. |
last update 2024-01-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-10-18formatting: failedlinting: failed |
0 |
4 |
||
A pipeline for processing 16S / ITS data |
last update 2021-10-27formatting: failedlinting: failed |
0 |
1 |
||
A simple snakemake workflow to align nanopore data using minimap2 |
last update 2024-02-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-02-03formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-02-01formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2024-01-31formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2024-01-19formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-12-18formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-12-26formatting: failedlinting: failed |
0 |
1 |
||
HPA single project, aiming for reproducibility using snakemake |
last update 2024-01-25formatting: failedlinting: failed |
0 |
1 |
||
Running logic for the indexing tasks for Bulk Expression Atlas |
last update 2023-01-23formatting: failedlinting: failed |
0 |
5 |
||
Developmental private RNASeq pipeline for bacterial quantification. |
last update 2024-01-25formatting: failedlinting: failed |
0 |
1 |
||
Repository for building IGSR data sets for use in VarFish |
genetics varfish variant-filtration variant-prioritization vcf |
last update 2024-01-24formatting: passedlinting: failed |
0 |
6 |
|
No description available. |
last update 2024-03-26formatting: failedlinting: failed |
0 |
1 |
||
RNA-Seq pipeline to compute the differential expression between the RNAs bound either by WT ribosome… |
last update 2023-06-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-01-22formatting: failedlinting: failed |
0 |
1 |
||
Small RNA-Seq analysis for Yan J., Ravisankar P., Zhao A., Li H., Oyler-Castrillo P., Solley S., Cha… |
crispr-analysis quarto rna-seq snakemake workflow |
last update 2024-01-22formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2023-11-18formatting: failedlinting: failed |
0 |
1 |
||
Companion code for the DFF-Seq methods paper DFF-ChIP: Probing the interaction of transcription fact… |
last update 2024-01-22formatting: failedlinting: failed |
0 |
1 |
||
Pipeline for processing single cell whole genome sequencing data |
last update 2024-01-12formatting: failedlinting: failed |
0 |
1 |
||
Snakemake & Singularity workflow for DNA-Seq using GATK Best Practices |
last update 2024-01-19formatting: failedlinting: failed |
0 |
1 |
||
tutorial for creating workflow in python |
last update 2024-01-18formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-07-16formatting: failedlinting: passed |
0 |
1 |
||
Accompanying code for analysis of manuscript in Nature Aging: Implications of stress-induced gene ex… |
bioinformatics cite-seq jupyter multiome quarto rna-seq |
last update 2024-01-16formatting: failedlinting: failed |
0 |
1 |
|
Part of the flow cytrometry QC model project, simulating artificial flow cytometry data |
last update 2024-01-15formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-08-23formatting: failedlinting: failed |
0 |
1 |
||
Target Illumina assembler |
last update 2024-01-15formatting: failedlinting: failed |
0 |
1 |
||
Code used for main bioinformatics workflow in Functional consequences of reductive protein evolution… |
last update 2024-01-15formatting: failedlinting: failed |
0 |
1 |
||
Pipeline for comparative genomics of Mycoplasma ovipneumoniae |
last update 2024-01-15formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-10-17formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-01-10formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-01-11formatting: failedlinting: failed |
0 |
1 |
||
Muscat comparison - v2 |
last update 2023-09-07formatting: failedlinting: failed |
0 |
2 |
||
AncFlow: A snakemake based pipeline for the ancestral sequence reconstruction of clustered phylogene… |
ancestral-sequence-reconstruction bioinformatics multiple-sequence-alignment phylogenetics |
last update 2024-02-21formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2022-12-19formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-02-15formatting: failedlinting: failed |
0 |
1 |
||
QC and trimming workflow for WGS illumina data |
last update 2021-11-15formatting: failedlinting: failed |
0 |
1 |
||
calling absolute copy numbers on single cell DNA sequencing data - stagging repo for public release |
last update 2023-07-27formatting: failedlinting: failed |
0 |
7 |
||
No description available. |
last update 2024-01-09formatting: failedlinting: failed |
0 |
2 |
||
Research on basal body temperature |
last update 2023-02-07formatting: failedlinting: failed |
0 |
2 |
||
Measuring and analysing people’s preferences about fully-renewable, European energy supply. |
last update 2024-01-08formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-11-04formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2023-12-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-01-05formatting: passedlinting: failed |
0 |
1 |
||
microRNA-seq workflow utilizing STAR to generate a Sample-Gene read count matrix |
last update 2023-08-25formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2023-10-25formatting: failedlinting: failed |
0 |
1 |
||
Snakemake implementation of pathogen classification from shotgun RNAseq data in dirty mice |
last update 2023-12-13formatting: failedlinting: failed |
0 |
1 |
||
This is a snakemake workflow of variant calling |
last update 2023-12-28formatting: failedlinting: failed |
0 |
1 |
||
snakemake example |
last update 2023-12-22formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for the processing of 16S rRNA gene-derived amplicon sequencing data |
last update 2023-12-22formatting: failedlinting: failed |
0 |
1 |
||
This is a Snakemake workflow that calculates maximum-likelihood gene trees with IQ-TREE and 100 boot… |
astral multispecies-coalescent snakemake species-tree workflow iq-tree maximum-likelihood |
last update 2023-04-21formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2023-12-21formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2024-03-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-12-09formatting: failedlinting: failed |
0 |
1 |
||
qiime2 asd scripts |
last update 2022-01-06formatting: failedlinting: failed |
0 |
1 |
||
An enhanced template structure for Snakemake |
git-bash reproducibility snakemake windows python make snakemake-workflow |
last update 2023-02-15formatting: failedlinting: failed |
0 |
1 |
|
A set of snakemake workflows and jupyter notebooks to benchmark the runtime, memory consumption, and… |
last update 2023-12-14formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-12-15formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for filtering, lifting over to hg38, and merging WGS gvcf files. |
last update 2022-06-26formatting: failedlinting: failed |
0 |
1 |
||
Software to track single cells with fluorescence in live cell imaging movies. |
last update 2023-12-14formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-02-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-09-21formatting: failedlinting: failed |
0 |
1 |
||
https://drmcrl.github.io/MFM-223_DHT-RNASeq/ |
last update 2023-12-13formatting: failedlinting: failed |
0 |
2 |
||
Analysis of TRIM–peptide simulations (multiple) |
last update 2023-12-13formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for t33b peptide analysis |
last update 2023-12-13formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for t33a peptide analysis |
last update 2023-12-13formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for t24 peptide analysis |
last update 2023-12-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-12-11formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-12-12formatting: failedlinting: failed |
0 |
1 |
||
A tool to perform functional enrichment analysis |
last update 2023-10-23formatting: failedlinting: failed |
0 |
1 |
||
Redcap surveys for WeCare |
last update 2024-02-07formatting: failedlinting: failed |
0 |
1 |
||
Integrated Mapping and Profiling of Allelically-expressed Loci with Annotations |
allele-specific-expression bioinformatics cancer snakemake-workflow |
last update 2023-10-20formatting: failedlinting: failed |
0 |
4 |
|
No description available. |
last update 2023-10-24formatting: failedlinting: failed |
0 |
0 |
||
Code to reproduce analyses in the Chapter 5(Making sense of noisy patient-derived data: novel method… |
last update 2023-08-01formatting: failedlinting: failed |
0 |
1 |
||
Pipeline for scaling crosscheck fingerprints for datasets with multiple samples per patient |
last update 2023-07-18formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for RNA-Seq analysis |
last update 2023-09-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-11-02formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-06-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-10-28formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-07-11formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake workflow for converting WSI from proprietary to open formats |
last update 2022-01-31formatting: failedlinting: failed |
0 |
12 |
||
No description available. |
last update 2023-10-24formatting: failedlinting: failed |
0 |
1 |
||
demultiplex RNA/ATAC bcl files and align multiomic RNA/ATAC reads with cellranger-arc using snakemak… |
last update 2023-12-11formatting: failedlinting: failed |
0 |
1 |
||
small RNA library processing and analysis |
snakemake-workflow srna loxodes |
last update 2023-10-25formatting: failedlinting: failed |
0 |
1 |
|
Pogigwasc gene prediction of Loxodes magnus genome |
snakemake-workflow genome-annotation gene-prediction loxodes |
last update 2023-10-25formatting: failedlinting: failed |
0 |
1 |
|
Empirical intron annotation for Loxodes magnus genome assembly |
snakemake-workflow genome-annotation intron-prediction loxodes |
last update 2023-10-25formatting: failedlinting: failed |
0 |
1 |
|
The Repository to download, STAR_align, TELESCOPE and Process DE for Mets vs. Non-mets TCGA CM Bulk-… |
last update 2023-10-18formatting: failedlinting: failed |
0 |
1 |
||
Creating a T5 model to detect hate speech/microagressions |
last update 2022-02-04formatting: failedlinting: failed |
0 |
1 |
||
assignment-2-python-refresher-FahsaiNak created by GitHub Classroom |
last update 2023-10-24formatting: failedlinting: failed |
0 |
1 |
||
This workflow is intended to parcellate the functional surface data given an atlas and save in .h5 f… |
last update 2023-11-08formatting: failedlinting: failed |
0 |
1 |
||
a short snakemake workflow to analyze bulk RNAseq data |
last update 2023-11-08formatting: failedlinting: failed |
0 |
1 |
||
Project 2 from SC2 @ FUB This project is currently still in progress, therefore the code is not cle… |
assembly consenus illumina nanopore snakemake |
last update 2023-09-28formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2023-06-26formatting: failedlinting: failed |
0 |
5 |
||
No description available. |
last update 2023-10-12formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2023-11-08formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2023-11-06formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-11-07formatting: failedlinting: failed |
0 |
1 |
||
singularity & snakemake workflow to detect mutations with several tools to detect mutations |
last update 2022-11-02formatting: failedlinting: failed |
0 |
1 |
||
Evaluates binding energies using varius tools |
last update 2023-09-29formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-11-05formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2023-08-24formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for the processing of RNAseq data |
rna-seq-analysis rna-seq-pipeline rnaseq snakemake |
last update 2023-10-20formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2023-02-08formatting: failedlinting: failed |
0 |
2 |
||
An ensemble structural variant calling pipeline driven by snakemake using DELLY, LUMPY, CNVNATOR and… |
last update 2023-01-26formatting: failedlinting: failed |
0 |
1 |
||
This workflow performs an RNA-seq analysis from the sequencing output data to the differential expre… |
rna-seq-analysis bulk-rna-seq |
last update 2021-10-20formatting: failedlinting: failed |
0 |
2 |
|
Automated pipeline for the PacBio IsoSeq3 workflow and follow up analyses |
last update 2023-11-10formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
biofilm bioinformatics feature-selection kmer-counting machine-learning population-structure salmonella snakemake xgboost |
last update 2023-11-06formatting: failedlinting: failed |
0 |
1 |
|
Code repository for the support project P_Snoeijs-Leijonmalm_2205 |
metagenomics |
last update 2023-11-09formatting: failedlinting: failed |
0 |
7 |
|
No description available. |
last update 2023-09-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-11-13formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2023-02-14formatting: passedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-11-12formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2023-11-12formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
snakemake-workflow genome-assembly loxodes |
last update 2023-11-10formatting: failedlinting: failed |
0 |
1 |
|
singularity & snakemake workflow to run a TROLL experiment. |
last update 2023-05-05formatting: failedlinting: failed |
0 |
1 |
||
Create a snakemake pipeline following the workflow outlined in the Variant Calling Workflow |
last update 2023-11-03formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-10-31formatting: failedlinting: failed |
0 |
1 |
||
whakapapa workflow for rakeiora |
last update 2023-11-20formatting: failedlinting: passed |
0 |
5 |
||
Bulk RNA-Seq analysis for Molly Brennan (Ploss Lab, Princeton) |
last update 2023-11-28formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
bioinformatics genome-assembly snakemake bbduk fastp unicycler checkm2 |
last update 2023-11-28formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2023-11-20formatting: failedlinting: failed |
0 |
1 |
||
Partial bioinformatic workflow for Figure 4c in : Differential prevalence and risk factors for infec… |
last update 2023-12-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-11-26formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2023-11-20formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2023-07-15formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-05-15formatting: failedlinting: failed |
0 |
2 |
||
A snakemake workflow introducing users to snakemake basics. Workflow goes from mapping reads, to sor… |
last update 2023-11-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-11-21formatting: passedlinting: failed |
0 |
1 |
||
Modified from tjbencomo/ngs-pipeline for Pitt CRC HTC |
last update 2023-11-20formatting: failedlinting: failed |
0 |
1 |
||
First complet version of the workflow with snakemake |
last update 2023-07-25formatting: failedlinting: passed |
0 |
3 |
||
Heatmap figures from CNV data from ASCAT files in GDC |
last update 2023-02-10formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-11-15formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-12-04formatting: failedlinting: failed |
0 |
0 |
||
Workflow that processes and annotates ParlaCLARIN corpus files |
last update 2021-12-16formatting: failedlinting: failed |
0 |
3 |
||
snakemake workflow using R scripts to pull precipitation/climate data for Davis |
last update 2021-12-30formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline to reproduce the results in the forthcoming paper One week ahead prediction of ha… |
data-science harmful-algal-blooms iowa iowastateuniversity snakemake machine-learning python r tidymodels classimbalance ensemble logistic-regression neural-network xgboost |
last update 2023-04-11formatting: failedlinting: passed |
0 |
2 |
|
A mini snakemake pipeline to batch construct consensus sequences from long nanopore amplicons w/ med… |
last update 2022-07-19formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-12-09formatting: failedlinting: failed |
0 |
1 |
||
IS 477 final project. Collaborating with Stefan Chu. |
last update 2023-12-09formatting: failedlinting: failed |
0 |
1 |
||
Private repository for IS477 Fall 2023 final project |
last update 2023-12-09formatting: failedlinting: failed |
0 |
1 |
||
Final Project for IS477 |
last update 2023-12-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-12-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-11-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-12-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-12-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-12-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-12-09formatting: failedlinting: failed |
0 |
1 |
||
A reproducible analysis based on IS 477 class materials |
last update 2023-12-08formatting: failedlinting: failed |
0 |
1 |
||
Phase imputed genotype data |
last update 2023-08-23formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-12-08formatting: failedlinting: failed |
0 |
1 |
||
is477-fall2023-final-project |
last update 2023-12-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-12-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-12-06formatting: failedlinting: failed |
0 |
1 |
||
A snakemake pipeline to extract miRNA precursor sequence and predict structure |
last update 2023-12-04formatting: failedlinting: failed |
0 |
1 |
||
IS 477 Final Project |
last update 2023-12-05formatting: failedlinting: failed |
0 |
1 |
||
Repository dedicated to the final project of the ReproHackaton course at the Paris Saclay University… |
last update 2023-12-04formatting: failedlinting: failed |
0 |
0 |
||
Final Project for IS-477 Fall 2023 |
last update 2023-12-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-12-19formatting: failedlinting: failed |
0 |
3 |
||
Single cell data from Germinal Center B cell paper |
last update 2023-08-18formatting: failedlinting: failed |
0 |
1 |
||
This is Andy’s workflow for finding MAGs in assemblies from separate samples including merging multi… |
last update 2022-10-14formatting: failedlinting: failed |
0 |
2 |
||
JasonCharamis/Snakemake-workflow-for-IQ-TREE-based-phylogenetic-analysis |
Snakemake pipeline for running fast maximum likelihood phylogenetic analyses using IQ-TREE2. Works w… |
last update 2023-05-24formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2023-07-14formatting: failedlinting: failed |
0 |
1 |
||
Snakemake and Singularity workflow to Downscale Climate Projections |
last update 2023-11-13formatting: failedlinting: failed |
0 |
1 |
||
Flattening annotation for bakR |
last update 2023-03-23formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-04-04formatting: failedlinting: failed |
0 |
1 |
||
Workflow to simulate SARS-CoV-2 amplicons and reads. |
last update 2022-05-27formatting: failedlinting: failed |
0 |
5 |
||
GATK4 Best practices workflow |
last update 2023-10-15formatting: failedlinting: failed |
0 |
1 |
||
Pipeline for scaling QTLtools mbv |
last update 2023-10-13formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for estimating genetic correlations between traits |
last update 2023-09-16formatting: failedlinting: failed |
0 |
0 |
||
ONT assembly pipeline |
last update 2023-02-08formatting: failedlinting: failed |
0 |
1 |
||
Bond Lattice Sampling and Analytical Approximation |
last update 2023-10-12formatting: failedlinting: failed |
0 |
3 |
||
This is a molecular model intended to identify inhibitors of the SRD5A2 threw out virtual screening. |
last update 2023-10-11formatting: failedlinting: failed |
0 |
1 |
||
This is a molecular model intended to identify inhibitors of the AKR1D1 threw out virtual screening. |
last update 2023-10-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-07-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-10-09formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2023-09-29formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-09-07formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for prokariotic genome assembly and annotation |
last update 2023-10-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-10-05formatting: failedlinting: failed |
0 |
0 |
||
A spatial analysis of measles virus variant dynamics in the brain. |
last update 2023-05-08formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-10-01formatting: failedlinting: failed |
0 |
1 |
||
This is a simple snakemake workflow for similarity search and phylogenetic analysis. |
last update 2023-10-03formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-07-26formatting: failedlinting: failed |
0 |
0 |
||
In this repository, we present the code for the analysis of study of the transcription’s impact on E… |
last update 2022-11-30formatting: failedlinting: failed |
0 |
1 |
||
Nevada-Bioinformatics-Center/snakemake_gbs_sorghum_mapping_workflow |
snakemake GBS sorghum mapping pipeline for sorghum data using bowtie2. |
last update 2022-06-23formatting: failedlinting: failed |
0 |
2 |
|
Analyzing Twist Targeted Methylation Sequencing Data Using the Twist Human Methylome Panel |
last update 2023-09-19formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2022-11-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-09-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-09-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-09-22formatting: failedlinting: failed |
0 |
1 |
||
Fast profiler using mmseqs |
last update 2023-09-27formatting: failedlinting: failed |
0 |
2 |
||
This workflow performs a metabarcoding analysis from the reads sequencing to the production of a rep… |
metabarcoding 16srrna qiime2-environment |
last update 2022-12-08formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2023-09-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-09-21formatting: failedlinting: failed |
0 |
1 |
||
Whole exome sequencing snakemake workflow based on GATK best practice |
bioinformatics bioinformatics-pipeline cli ngs-analysis ngs-pipeline python3 gatk-bestpractices genomics snakemake snakemake-workflow wes |
last update 2023-06-15formatting: failedlinting: failed |
0 |
3 |
|
A snakemake workflow to generate multiple synthetic datasets using aMGSIM |
last update 2022-06-17formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2023-09-23formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-07-18formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-08-07formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake pipeline for RNASeq data analysis |
last update 2023-09-21formatting: failedlinting: passed |
0 |
0 |
||
Workflow to detect and taxonomically annotate virus in metagenomes |
last update 2023-09-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-08-18formatting: failedlinting: failed |
0 |
2 |
||
snakemake pipeline for creating trees from sequence sets |
last update 2023-01-27formatting: failedlinting: failed |
0 |
6 |
||
No description available. |
last update 2022-08-23formatting: failedlinting: failed |
0 |
1 |
||
GAF annotation experiment for the HPRC 2023 Annual Meeting |
last update 2023-09-09formatting: failedlinting: failed |
0 |
1 |
||
KZ PyPSA for base and zero carbon |
last update 2023-09-15formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-06-24formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-07-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-03-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-07-06formatting: failedlinting: failed |
0 |
1 |
||
Application of the OptiFit algorithm to CRC dataset to predict SRNs from microbiome data |
last update 2023-07-05formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2023-01-25formatting: failedlinting: failed |
0 |
1 |
||
Snakemake implementation of data pre-processing for variant discovery from GATK Best Practices Workf… |
last update 2023-07-05formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow that checks the scalability of LAMMPS run on a cluster |
last update 2023-06-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-02-17formatting: failedlinting: passed |
0 |
2 |
||
No description available. |
last update 2022-10-12formatting: failedlinting: failed |
0 |
2 |
||
SnakeMake workflow for the processing of EMseq data |
last update 2023-06-30formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-06-23formatting: failedlinting: failed |
0 |
1 |
||
contains examples of various snakemake features |
last update 2023-06-29formatting: failedlinting: failed |
0 |
3 |
||
Code for publication |
last update 2023-04-15formatting: failedlinting: failed |
0 |
2 |
||
ChIP-seq |
last update 2022-02-18formatting: failedlinting: failed |
0 |
2 |
||
A snakemake workflow for analysing synonymous and nonsynonymous mutations |
last update 2023-06-29formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-01-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-04-03formatting: failedlinting: failed |
0 |
1 |
||
Conversion workflow for EEG data |
last update 2023-06-21formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-02-09formatting: failedlinting: failed |
0 |
5 |
||
No description available. |
last update 2023-06-28formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-05-27formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-05-04formatting: failedlinting: failed |
0 |
1 |
||
Detect known and unknown splicing events and test for difference across conditions |
last update 2022-10-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-11-10formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-05-24formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-06-22formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-06-22formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-06-16formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-06-20formatting: failedlinting: failed |
0 |
2 |
||
Snakemake workflow for downloading and converting MRI data to BIDS |
last update 2023-06-21formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-06-21formatting: failedlinting: failed |
0 |
2 |
||
MacroConf Dataset & Workflows to Assess Cyclic Peptide Solution Structures |
amber molecular-dynamics nmr-spectroscopy snakemake cyclic-peptides |
last update 2023-03-28formatting: failedlinting: failed |
0 |
1 |
|
Snakemake module containing steps to minimize big files prior to storage |
last update 2022-03-09formatting: failedlinting: failed |
0 |
3 |
||
Bash scripts for running QIIME 1.9 and a Snakemake workflow to automate it using singularity contain… |
microbiome-analysis qiime singularity-containers |
last update 2023-06-20formatting: failedlinting: failed |
0 |
1 |
|
A snakemake pipeline to assemble and annotate near full length 16S rRNA sequences. |
last update 2023-06-20formatting: failedlinting: failed |
0 |
1 |
||
A metagenomics pipeline for analyzing antimicrobial resistance developed for the FOREWARN project |
last update 2023-05-16formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-01-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-06-06formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-06-16formatting: failedlinting: failed |
0 |
1 |
||
This is a template for Snakemake workflows on the new Slurm HPC at VAI. |
last update 2023-06-16formatting: failedlinting: failed |
0 |
1 |
||
This repository is intended to store our pipeline for marker genes analysis. |
last update 2022-08-18formatting: failedlinting: failed |
0 |
5 |
||
No description available. |
last update 2023-05-30formatting: failedlinting: failed |
0 |
2 |
||
Bacterial wg-GWAS for the detection of E. coli BSI and commensal genetic determinants |
gwas microbial-genomics |
last update 2022-12-08formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2023-01-18formatting: failedlinting: failed |
0 |
1 |
||
Pipeline for analyzing short read bulk RNAseq data |
last update 2022-01-13formatting: failedlinting: failed |
0 |
1 |
||
A snakemake pipeline for tick determination from ONT whole genome sequencing samples. |
bioinformatics-pipeline snakemake species-identification whole-genome-sequencing |
last update 2023-06-12formatting: failedlinting: failed |
0 |
1 |
|
You assembled a genome and now you want to annotate it with genes, proteins motifs etc. |
last update 2022-10-04formatting: failedlinting: failed |
0 |
1 |
||
SV calling using multiple software tools with results evaluated using the Jaccard Index Measure |
last update 2023-03-06formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-06-29formatting: failedlinting: failed |
0 |
1 |
||
Get climatic data from ERA5-Land on CDS using python cdsapi |
last update 2023-06-09formatting: failedlinting: failed |
0 |
1 |
||
Source code for the characterization of new genes paper published in NAR. |
last update 2023-06-07formatting: failedlinting: failed |
0 |
2 |
||
repository for comparing DNA Binding Sites for motif selection |
last update 2023-06-07formatting: passedlinting: failed |
0 |
1 |
||
Dovetail Clover Genome (DCG): Generating reference assembly and annotation for white clover (Trifoli… |
last update 2023-06-06formatting: failedlinting: failed |
0 |
1 |
||
Workflow to generate cisTarget database for urchins |
last update 2022-08-23formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-06-02formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-06-06formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2022-11-03formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-07-27formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2022-04-21formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-11-19formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-04-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-12-06formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-06-01formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-02-10formatting: failedlinting: failed |
0 |
4 |
||
singularity & snakemake workflow to annotate genomes. |
last update 2022-05-24formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-05-30formatting: failedlinting: failed |
0 |
1 |
||
Workflow for detecting PMCs in confocal images |
last update 2022-08-01formatting: passedlinting: failed |
0 |
1 |
||
Created for testing the metabolomics pipeline through snakemake |
last update 2022-08-01formatting: failedlinting: passed |
0 |
3 |
||
Assembly pipeline for 10X chromium genomes of Mytilus species |
last update 2022-01-14formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2022-01-05formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-03-21formatting: failedlinting: failed |
0 |
1 |
||
A snakemake workflow to simulate ASE data for validation purposes. |
bioinformatics genetics |
last update 2023-05-18formatting: failedlinting: failed |
0 |
2 |
|
No description available. |
last update 2023-04-09formatting: failedlinting: failed |
0 |
1 |
||
Podacris Genome Annotation (PGA) |
last update 2023-05-23formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-05-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-01-05formatting: failedlinting: failed |
0 |
4 |
||
No description available. |
last update 2022-08-15formatting: failedlinting: passed |
0 |
1 |
||
Macaque brain reconstruction snakemake workflow |
last update 2023-05-19formatting: failedlinting: failed |
0 |
2 |
||
This repository contains all the code that was used by Cristian Riccio in the Burton et al. 2019 pap… |
last update 2022-12-07formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2023-05-19formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-06-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-03-21formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2023-05-15formatting: failedlinting: failed |
0 |
1 |
||
create consensus sequence from Oxford Nanopore Technologies (ONT) amplicon sequencing |
last update 2023-03-28formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2023-04-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-05-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-05-12formatting: failedlinting: failed |
0 |
1 |
||
A Snakelike workflow to generate unique FASTQ files |
last update 2023-05-12formatting: failedlinting: failed |
0 |
9 |
||
No description available. |
last update 2023-05-12formatting: failedlinting: passed |
0 |
1 |
||
A snakemake workflow to run breseq with SAR-CoV2 samples and concatenate the resulting data for down… |
last update 2023-05-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-04-16formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for annotating VCF files |
last update 2022-08-16formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-05-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-05-09formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2023-05-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-05-07formatting: failedlinting: failed |
0 |
2 |
||
Behavioral Genetics in Drosophila: RNA-Seq analysis pipeline |
last update 2022-06-03formatting: failedlinting: failed |
0 |
2 |
||
Build repository for reference container |
last update 2022-08-09formatting: failedlinting: failed |
0 |
1 |
||
singularity & snakemake workflow template. |
last update 2023-05-05formatting: failedlinting: failed |
0 |
1 |
||
A snakemake workflow for bulk RNA-seq data preprocessing including sequence alignment, quality check… |
last update 2022-11-01formatting: failedlinting: failed |
0 |
2 |
||
Workflow for reencrypting and sending CRCC data |
last update 2022-01-20formatting: failedlinting: failed |
0 |
13 |
||
A snakemake based workflow for ChIPSeq data analysis |
snakemake snakemake-workflows chipseq |
last update 2021-11-29formatting: failedlinting: failed |
0 |
2 |
|
No description available. |
last update 2023-05-03formatting: failedlinting: failed |
0 |
1 |
||
A Pipeline for comparing GATK and Deepvariant |
last update 2023-05-03formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2023-05-03formatting: failedlinting: failed |
0 |
1 |
||
This software can be used to analyse Ont-Monkeypox data. |
last update 2022-11-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-05-01formatting: failedlinting: failed |
0 |
0 |
||
Snakemake workflows for microbiome data analysis |
last update 2023-03-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-11-27formatting: failedlinting: failed |
0 |
1 |
||
Mutational antigenic profiling of Adimab antibodies in the Omicron BA.1 background |
last update 2023-04-19formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-03-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-01-10formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-02-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-04-24formatting: failedlinting: failed |
0 |
1 |
||
Snakemake tutorial for C-SCALE |
last update 2022-11-07formatting: failedlinting: passed |
0 |
7 |
||
Pipeline to process duplex sequencing data. |
last update 2022-01-11formatting: failedlinting: failed |
0 |
1 |
||
Variant calling pipeline for identifying gremline and somatic mutations in patient genomes. |
last update 2023-04-15formatting: failedlinting: failed |
0 |
1 |
||
Twitch Chat Analysis Pipeline |
last update 2023-04-11formatting: passedlinting: passed |
0 |
1 |
||
Snakemake pipeline for processing 10x scRNAseq data on a SLURM cluster |
last update 2022-06-17formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow to de novo assemble transcriptomes with two software, Trinity and Shannon. Import… |
rna-seq shannon snakemake transcriptome-assembly trinity workflow |
last update 2023-04-21formatting: failedlinting: failed |
0 |
1 |
|
Snakemake workflow that concatenate MSA files into a supermatrix and calculates a maximum likelihood… |
iq-tree maximum-likelihood snakemake supermatrix-phylogenetic-analyses workflow |
last update 2023-04-21formatting: failedlinting: failed |
0 |
1 |
|
simple pangraph tutorial for WCS conference |
last update 2023-04-21formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-12-20formatting: failedlinting: failed |
0 |
2 |
||
Simple workflow for single subject dicom archive to bids |
last update 2023-04-19formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-04-06formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for detecting CR6 or CW3 viral variants. |
last update 2023-04-13formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2023-04-14formatting: failedlinting: failed |
0 |
4 |
||
No description available. |
last update 2023-04-14formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-04-14formatting: failedlinting: failed |
0 |
2 |
||
Final assignment Dataprocessing course 2022-2023 |
last update 2023-03-28formatting: failedlinting: passed |
0 |
1 |
||
A snakemake pipeline to extract Type I RM system components and cluster hsdS genes from Xylella fast… |
last update 2023-04-12formatting: failedlinting: failed |
0 |
1 |
||
Repo for final assignment dataprocessing course |
last update 2023-04-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-12-15formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-04-10formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake based modular Workflow that facilitates RNA-Seq analyses with a special focus on splici… |
last update 2023-03-23formatting: failedlinting: failed |
0 |
1 |
||
A brief and simple snakemake tutorial |
last update 2023-04-06formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-12-25formatting: failedlinting: failed |
0 |
1 |
||
Snakemake based pipeline for atacseq dataanalysis |
last update 2023-03-23formatting: failedlinting: failed |
0 |
2 |
||
Demographic analysis for carrot populations |
last update 2021-12-07formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2023-03-31formatting: failedlinting: failed |
0 |
1 |
||
intro lecture for Social Media and Web Analytics |
last update 2022-03-27formatting: failedlinting: failed |
0 |
2 |
||
A snakemake pipeline to generate the transcriptomic signatures of drug susceptibility used in beyond… |
last update 2023-02-20formatting: failedlinting: failed |
0 |
0 |
||
Snakemake workflow for dada2 analysis of the data |
last update 2023-03-27formatting: failedlinting: failed |
0 |
1 |
||
Postprocessing workflow for the wrf-hydro runs and figures in The application and modification of WR… |
last update 2023-04-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-03-31formatting: failedlinting: failed |
0 |
1 |
||
This is a repository holding code to obtain preliminary results for the VR Starting Grant 2023. |
last update 2023-03-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-03-25formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-02-03formatting: failedlinting: failed |
0 |
1 |
||
Sars-CoV-2 Lineage Determination homework for cancer genomics course |
last update 2023-03-23formatting: failedlinting: failed |
0 |
1 |
||
liliab98/snakemake-workflow-scRNA-seq-cell-to-embryo-deconvolution |
No description available. |
last update 2023-05-04formatting: passedlinting: failed |
0 |
1 |
|
Extension of rna-seq-star-deseq2 Snakemake workflow to process NR-seq data for bakR |
last update 2023-02-16formatting: failedlinting: passed |
0 |
1 |
||
Design primers for mutagenesis to create spike libraries |
last update 2023-03-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-10-18formatting: failedlinting: failed |
0 |
0 |
||
RNA-Seq data pre-processing Snakemake Pipeline for BMI Lab, SNUH |
last update 2023-03-06formatting: failedlinting: failed |
0 |
0 |
||
Snakemake workflows for SCIP use cases. |
last update 2022-11-03formatting: failedlinting: failed |
0 |
1 |
||
A snakemake workflow to create reference indices and other supplementary files for analysis |
snakemake snakemake-workflow |
last update 2023-03-09formatting: failedlinting: failed |
0 |
2 |
|
Batch submit workflow for snakedwi |
last update 2022-12-23formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-12-07formatting: failedlinting: failed |
0 |
1 |
||
Julia package for ice floe tracker |
last update 2023-05-23formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2023-01-12formatting: failedlinting: failed |
0 |
2 |
||
Enterovirus-D68 phylogenetic analyses code - actively maintained |
last update 2022-02-14formatting: failedlinting: failed |
0 |
10 |
||
simple RNAseq pipeline based on snakemake workflow with extensive QC |
last update 2021-10-29formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-03-03formatting: failedlinting: failed |
0 |
1 |
||
GATK Variant Quality Score Recalibration for filtering variant calling set |
last update 2023-03-02formatting: failedlinting: failed |
0 |
1 |
||
pd410668/Analysis_of_multi_way_chromatin_interactions_from_very_long_sequencing_reads |
No description available. |
last update 2022-01-04formatting: failedlinting: failed |
0 |
2 |
|
Snakemake pipeline for running FACETS on all WXS TCGA samples. |
last update 2023-03-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-03-01formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-04-25formatting: failedlinting: failed |
0 |
1 |
||
Metagenome-Assembled Genome Analysis of Gut Microbiota |
last update 2023-05-21formatting: failedlinting: failed |
0 |
2 |
||
Reference library for microorganisms with different genome assembly metrics and statistics |
last update 2023-02-23formatting: failedlinting: failed |
0 |
3 |
||
Snakemake workflow for RAD novaseq data |
last update 2023-02-27formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for Autoscience n-heptane model |
last update 2022-08-26formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake workflow to analyse and visualise Illumina Infinium Methylation arrays |
last update 2022-02-25formatting: failedlinting: passed |
0 |
1 |
||
propanet snakemake |
last update 2023-02-21formatting: failedlinting: failed |
0 |
1 |
||
snakemake pipeline to demultiplex PacBio reads using Index sequences added during PCR |
last update 2023-02-23formatting: failedlinting: failed |
0 |
4 |
||
No description available. |
last update 2022-06-06formatting: failedlinting: failed |
0 |
1 |
||
|
last update 2023-02-21formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-02-23formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-02-23formatting: failedlinting: failed |
0 |
2 |
||
showyourwork_globus_demo |
last update 2023-02-22formatting: passedlinting: passed |
0 |
2 |
||
No description available. |
last update 2023-02-21formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-02-20formatting: failedlinting: failed |
0 |
1 |
||
An example research project with Snakemake & git lfs |
last update 2023-02-20formatting: failedlinting: failed |
0 |
1 |
||
Meet-EU project (Orange team) |
last update 2023-02-06formatting: failedlinting: failed |
0 |
1 |
||
RNAseq workflow using snakemake |
last update 2023-02-19formatting: failedlinting: failed |
0 |
1 |
||
Updated version of a variant calling workflow implemented in Snakemake |
bioinformatics ngs pipeline workflow |
last update 2023-02-13formatting: failedlinting: failed |
0 |
1 |
|
Snakemake workflow to run cellranger on multiple samples within the ODCF database |
last update 2023-01-31formatting: failedlinting: failed |
0 |
4 |
||
Remove human contamination and functional analysis |
last update 2023-01-24formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for running inStrain on metagenomes |
last update 2021-05-22formatting: failedlinting: failed |
0 |
1 |
||
Using haptools to investigate factors affecting portability of PRSs |
last update 2023-02-13formatting: failedlinting: failed |
0 |
2 |
||
Forked from https://gitlab.com/data-analysis5/dna-sequencing/54gene-wgs-germline |
last update 2023-02-14formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-02-09formatting: failedlinting: failed |
0 |
0 |
||
Workflow for screening massive amounts of small molecules (ligands) against a target (PDB-File) |
last update 2022-12-16formatting: failedlinting: failed |
0 |
1 |
||
build NCBI lineages file for sourmash taxonomy |
last update 2023-02-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-02-08formatting: failedlinting: failed |
0 |
1 |
||
Showyourwork repository for Astro 511 Galaxies hw2 Winter quarter 2023 |
last update 2023-02-08formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake workflow for identifying a Sars-CoV-2 lineage from a paired-end read. It implements both… |
bioinformatics python snakemake sars-cov-2 |
last update 2023-02-08formatting: failedlinting: failed |
0 |
1 |
|
using twitter academic api to get tweets about R U Okay day |
last update 2021-10-01formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2022-08-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-02-05formatting: failedlinting: failed |
0 |
1 |
||
VESPA (Virtual Enrichment-based Signaling Protein-activity Analysis) signaling network inference mod… |
last update 2023-02-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-02-05formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow to test μ-PBWT against PBWT and Syllable-PBWT |
1000genomes pbwt snakemake |
last update 2023-02-03formatting: failedlinting: failed |
0 |
1 |
|
A simple workflow that creates a dereplicated KEGG GENES database by KO. |
last update 2023-02-03formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-02-02formatting: failedlinting: failed |
0 |
1 |
||
Analysis and results for the haptools manuscript |
last update 2023-01-18formatting: failedlinting: failed |
0 |
4 |
||
Code and workflows for adding content to the content registry. |
last update 2022-08-22formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2023-01-11formatting: failedlinting: failed |
0 |
1 |
||
This repository describes the project workflow that is being used at Kirdok Lab. |
last update 2023-01-25formatting: failedlinting: failed |
0 |
1 |
||
This is a record of my efforts to get snakemake to run on Azure Kubernetes Service. Works as of 2023… |
last update 2023-01-31formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-01-31formatting: failedlinting: failed |
0 |
1 |
||
Deep mutational scanning of the MERS and PDF-2180 CoV receptor-binding domains |
last update 2023-03-13formatting: failedlinting: failed |
0 |
1 |
||
Analysis of LMP foils data |
last update 2022-12-06formatting: failedlinting: failed |
0 |
1 |
||
Pipeline to identify the abundance determinants of human snoRNAs. |
last update 2022-08-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-11-01formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2023-02-09formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2022-05-05formatting: failedlinting: failed |
0 |
1 |
||
Commandline Snakemake workflow to assemble and query short haplotype genomes. |
bioinformatics sequencing genomics |
last update 2022-03-19formatting: failedlinting: failed |
0 |
2 |
|
No description available. |
last update 2022-11-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-01-31formatting: failedlinting: failed |
0 |
1 |
||
Analysis of p value sets submitted to NCBI GEO database as supplementary files |
p-values reproducibility ht-seq differential-expression snakemake |
last update 2021-11-15formatting: failedlinting: failed |
0 |
4 |
|
No description available. |
last update 2023-04-03formatting: passedlinting: failed |
0 |
2 |
||
Code for the manuscript Machine learning reveals STAT motifs as predictors for GR-mediated gene repr… |
last update 2023-01-18formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-01-23formatting: failedlinting: failed |
0 |
1 |
||
This is the record of process that to setup/write and use snakemake workflow to analysis RNAseq data… |
last update 2023-01-21formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-07-14formatting: failedlinting: failed |
0 |
1 |
||
Meeting Snakemake |
snakemake |
last update 2023-01-14formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2023-01-19formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-10-09formatting: failedlinting: failed |
0 |
1 |
||
A workflow for m6A data analysis |
last update 2022-02-18formatting: failedlinting: failed |
0 |
1 |
||
Paired-end CUT and RUN data processing workflow designed for execution on the BigPurple HPC. Primary… |
workflow cutandrun-seq |
last update 2022-01-28formatting: failedlinting: failed |
0 |
1 |
|
Paired-end ChIPseq data processing workflow designed for execution on the BigPurple HPC. Primary sof… |
pipeline workflow chip-seq-pipelines |
last update 2022-01-28formatting: failedlinting: failed |
0 |
1 |
|
Paired-end RNAseq data processing workflow designed for execution on the BigPurple HPC. This version… |
rna-seq pipeline |
last update 2022-01-28formatting: failedlinting: failed |
0 |
1 |
|
Paired-end RNAseq data processing workflow designed for execution on the BigPurple HPC. Primary soft… |
rna-seq pipeline |
last update 2022-01-28formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2022-01-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-01-24formatting: failedlinting: failed |
0 |
1 |
||
RNA-Seq Snakemake Workflow |
last update 2023-01-16formatting: failedlinting: failed |
0 |
1 |
||
Bacterial genome assembly and prediction -snakemake |
last update 2022-11-16formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-01-26formatting: failedlinting: failed |
0 |
4 |
||
Snakemake pipeline to assemble ONT reads |
last update 2023-01-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-06-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-10-03formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-12-08formatting: failedlinting: failed |
0 |
6 |
||
Barcoded pdmH1N1 virus hashing experiment |
last update 2022-10-08formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2022-12-19formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for batch job submission with hippunfold container |
last update 2022-09-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-01-06formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-04-04formatting: failedlinting: failed |
0 |
1 |
||
Workflow designed for Download, QC, Assemble, Variant calling, and Annotate bacterial WGS in batch |
bacterial-genomes snakemake whole-genome-sequencing |
last update 2022-12-21formatting: failedlinting: failed |
0 |
2 |
|
No description available. |
last update 2023-01-03formatting: failedlinting: failed |
0 |
2 |
||
Phaeocystis viruses |
last update 2023-01-03formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2022-04-08formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-12-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-10-31formatting: failedlinting: failed |
0 |
1 |
||
Example workflow for snakemake azure batch example workflow |
last update 2022-12-28formatting: failedlinting: failed |
0 |
1 |
||
The objective of this project is to use ML to determine if a weather patterns are synchronized on an… |
last update 2022-12-23formatting: failedlinting: failed |
0 |
1 |
||
Virome piepline for aDNA |
last update 2022-12-20formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for SM-PATseq |
pacbio pacbio-sequencing poly-a polyadenylation rna-seq |
last update 2023-01-13formatting: failedlinting: failed |
0 |
2 |
|
No description available. |
last update 2022-05-25formatting: failedlinting: failed |
0 |
1 |
||
General-purpose Snakemake workflow for diffusion-based subcortical parcellation |
last update 2022-11-10formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2022-12-19formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for NBIS SMS 6439 |
last update 2022-12-19formatting: failedlinting: failed |
0 |
1 |
||
ATAC-Seq Workflow built with Snakemake |
last update 2022-12-16formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2022-12-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-12-12formatting: failedlinting: failed |
0 |
1 |
||
Term project for BIOF 501 |
last update 2022-12-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-12-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-03-01formatting: failedlinting: failed |
0 |
1 |
||
Snakemake Workflow for ATACSeq (Paired-end) |
last update 2022-08-03formatting: failedlinting: failed |
0 |
1 |
||
This snakemake workflow imports a single fasta file with query sequences and blasts these against su… |
last update 2022-03-14formatting: failedlinting: failed |
0 |
1 |
||
Mutational antigenic profiling of the yeast-displayed Omicron BA.1 RBD for LY-CoV1404 mAb binding |
last update 2022-09-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-12-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-12-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-11-08formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-08-24formatting: failedlinting: failed |
0 |
3 |
||
Project – A Metagenomic Screening of Soil Microbiome |
last update 2023-01-31formatting: failedlinting: failed |
0 |
2 |
||
Repo for running custom snakemake for IBDne |
last update 2022-12-01formatting: failedlinting: failed |
0 |
4 |
||
Snakemake workflow to download the TGIRT-Seq datasets from GEO from multiple species and analyze the… |
last update 2022-11-30formatting: failedlinting: failed |
0 |
1 |
||
pipeline to process foursu timecourse data |
last update 2021-12-10formatting: failedlinting: failed |
0 |
0 |
||
Build indices for STAR, Kallisto etc. Add data for specified spike-in RNAs. |
last update 2021-12-06formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-08-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-11-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-02-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-11-26formatting: failedlinting: failed |
0 |
1 |
||
Snakemake ChIP-seq pipeline with singularity |
last update 2022-11-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-11-24formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-01-12formatting: failedlinting: failed |
0 |
5 |
||
No description available. |
last update 2022-08-19formatting: failedlinting: failed |
0 |
1 |
||
analysis of NGS data to build sars2 consensus sequences |
last update 2022-11-21formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-06-18formatting: failedlinting: failed |
0 |
2 |
||
Template for Snakemake workflows |
last update 2022-03-09formatting: passedlinting: passed |
0 |
1 |
||
🦆 Quality Control of WGS and exome samples 🦆 |
last update 2023-02-01formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2022-11-21formatting: passedlinting: passed |
0 |
1 |
||
SARS-CoV-2 spike mutation analysis |
last update 2022-11-19formatting: failedlinting: failed |
0 |
0 |
||
analyzing haplotype-specific DNA methylation from long-read data |
last update 2022-11-18formatting: failedlinting: failed |
0 |
1 |
||
Repository for the Snakemake ATAC-seq pipeline, using singularity to run |
last update 2022-11-08formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-11-15formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2023-01-26formatting: failedlinting: failed |
0 |
1 |
||
Bio 470 project 2022. Bulk RNA scripts |
last update 2022-11-15formatting: failedlinting: failed |
0 |
1 |
||
Forked from https://gitlab.com/data-analysis5/dna-sequencing/54gene-wgs-germline |
last update 2022-10-06formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-11-09formatting: failedlinting: failed |
0 |
1 |
||
Infinium QC Array workflow |
last update 2022-08-05formatting: failedlinting: failed |
0 |
4 |
||
Given a set of genomes, use a core genome database to construct alignments as input to adapt. |
last update 2022-11-03formatting: failedlinting: failed |
0 |
1 |
||
singularity & snakemake workflow to generate in silico mutations. |
last update 2022-11-02formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow to consolidate basic genome assembly benchmarking |
last update 2022-11-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-10-31formatting: failedlinting: failed |
0 |
1 |
||
A snakemake pipeline wrapping MitoZ and getOrganelle for de novo mitogenome assembly using short rea… |
mitochondria genome-assembly mitogenome snakemake mitochondrial-genome-assembly |
last update 2022-10-27formatting: failedlinting: failed |
0 |
1 |
|
Tooling & workflows for HK Twitter analysis |
last update 2023-01-21formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2022-10-26formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2022-10-04formatting: failedlinting: failed |
0 |
3 |
||
Snakemake based RNA_pipeline for running on WEXAC cluster |
last update 2022-11-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-10-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-10-25formatting: failedlinting: failed |
0 |
1 |
||
A snakemake workflow for trimming adapter sequences and quality filtering NGS reads using fastp. |
last update 2022-10-25formatting: failedlinting: failed |
0 |
1 |
||
Data analysis for the HWW metagenomes from Benin, Burkina Faso and Finland (AMRIWA project) |
last update 2023-01-18formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-10-25formatting: failedlinting: failed |
0 |
1 |
||
RNA-seq SNP based Phylogenetic Tree pipeline packaged as Snakemake workflow |
last update 2022-10-18formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-06-27formatting: failedlinting: failed |
0 |
1 |
||
A scalable workflow for discovering single-copy orthologs between species and aligning domain archit… |
last update 2023-01-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-10-23formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2022-09-23formatting: failedlinting: failed |
0 |
2 |
||
Snakemake workflow to perform tandem mass tag (TMT) analysis using the Trans Proteomic Pipeline (TPP… |
last update 2022-09-08formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for preprocessing fast files |
configuration-files fastq snakemake-workflows |
last update 2022-10-20formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2022-10-20formatting: failedlinting: failed |
0 |
1 |
||
Template snakemake project for the analysis of ATAC-Seq data |
last update 2022-08-08formatting: failedlinting: failed |
0 |
1 |
||
Using Snakemake to create a workflow to filter and trim sequence reads from a fastq file using fastp… |
last update 2022-10-18formatting: failedlinting: failed |
0 |
1 |
||
Deep Learning single-cell Identification and Annotation |
cell-type-identification deep-learning singularity snakemake single-cell-rna-seq |
last update 2022-10-18formatting: failedlinting: passed |
0 |
1 |
|
No description available. |
last update 2022-10-17formatting: failedlinting: failed |
0 |
1 |
||
A pipeline for long-read UMI/PID sequencing of HIV amplicons. |
last update 2022-09-05formatting: failedlinting: failed |
0 |
5 |
||
No description available. |
last update 2022-07-28formatting: failedlinting: failed |
0 |
1 |
||
Flags sequences that are entirely composed of tandem repeats |
last update 2022-01-15formatting: failedlinting: failed |
0 |
2 |
||
Code used for the manuscript ‘Network reconstruction for trans acting genetic loci using multi-omics… |
hotspots network-inference qtl simulation |
last update 2022-10-05formatting: failedlinting: failed |
0 |
0 |
|
Simple bare-bones snakebids+snakemake workflow example (not a BIDS app) |
last update 2022-10-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-09-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-08-23formatting: failedlinting: failed |
0 |
4 |
||
From the snakemake-workflows / single-cell-rna-seq. |
last update 2022-09-29formatting: failedlinting: passed |
0 |
1 |
||
Quantify signal in HCR FISH images |
last update 2022-06-21formatting: passedlinting: failed |
0 |
1 |
||
Internal imputation pipeline using snakemake |
last update 2021-12-15formatting: failedlinting: failed |
0 |
1 |
||
Steps to do preprocessing of single cell data |
last update 2022-03-23formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-09-29formatting: passedlinting: failed |
0 |
0 |
||
Snakemake workflow for benchmarking synthetic cytometry data |
last update 2022-09-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-09-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-07-26formatting: failedlinting: failed |
0 |
1 |
||
This is a full snakemake pipeline for somatic-combiner. |
last update 2022-01-07formatting: failedlinting: failed |
0 |
4 |
||
rose genome segmentation by ancestry indentification |
last update 2022-09-19formatting: failedlinting: failed |
0 |
1 |
||
Quantify HERVs in single nucleus RNA-seq GTEx datasets using single-cell Telescope (scTelescope) |
last update 2021-12-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-07-20formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipelines for replicating sstar analysis |
last update 2022-06-15formatting: failedlinting: failed |
0 |
1 |
||
Lecture 3 of DSMS. Topic: Regression |
last update 2022-09-15formatting: failedlinting: failed |
0 |
0 |
||
Lecture 2 of DSMS. Topic: Experimentation |
last update 2022-09-13formatting: failedlinting: failed |
0 |
0 |
||
Read-mapping against the contig catalogue from metagenomics by illumina and nanopore |
last update 2022-09-12formatting: failedlinting: failed |
0 |
1 |
||
Private github repository for Insect Biome Atlas project |
last update 2022-09-13formatting: failedlinting: failed |
0 |
3 |
||
Snakemake pipeline to perform a high-performance batch RNA-seq quantification |
bioinformatics python snakemake-workflow workflow-management |
last update 2022-09-14formatting: failedlinting: failed |
0 |
1 |
|
Analyses, experiments, and evaluations for the TrialMDP method |
clinical-trials dynamic-programming markov-decision-process snakemake |
last update 2021-10-01formatting: failedlinting: failed |
0 |
2 |
|
This repository contains the source code necessary to analyze DArTseqMet data, identifying the DNA m… |
last update 2022-09-09formatting: failedlinting: failed |
0 |
2 |
||
Generic RNA-seq quant for OGVFB group |
last update 2022-12-05formatting: failedlinting: failed |
0 |
1 |
||
RepCounter provides a lightweight, modular program for estimating the relative abundance of repeat f… |
last update 2022-09-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-09-02formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2022-09-01formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-01-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-08-02formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for fsleyes segmentation snapshots |
last update 2022-08-23formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-08-29formatting: failedlinting: failed |
0 |
1 |
||
Metatranscriptomics - snakemake pipeline as part of the Bpexa HS Leiden bioinformatics project |
last update 2022-08-29formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-12-28formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2022-07-15formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake workflow for the MSCi framework in BP&P |
last update 2022-08-18formatting: failedlinting: failed |
0 |
1 |
||
BAM or CRAM file to pair end FASTQ |
last update 2022-08-19formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-04-19formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-08-18formatting: failedlinting: failed |
0 |
3 |
||
scRNA-seq with unbiased metagenome quantification |
last update 2022-07-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-08-01formatting: failedlinting: failed |
0 |
1 |
||
Description of the microbiome of the Barfusser mummy of Basel |
last update 2022-07-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-08-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-08-12formatting: failedlinting: failed |
0 |
1 |
||
🐍 |
last update 2022-07-26formatting: passedlinting: failed |
0 |
1 |
||
Snakemake workflow to setup data sources |
last update 2021-11-09formatting: failedlinting: passed |
0 |
0 |
||
Snakemake wrapper for bacterial genome assembly from Illumina reads. |
last update 2022-07-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-06-07formatting: failedlinting: failed |
0 |
1 |
||
Nextstrain analysis of Norovirus |
last update 2022-06-23formatting: failedlinting: failed |
0 |
2 |
||
Repo for my master’s thesis |
last update 2022-07-16formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2022-07-07formatting: failedlinting: failed |
0 |
1 |
||
Repository for the Microbiology Resource Announcements paper on five complete Streptococcus suis gen… |
last update 2022-08-02formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2022-08-01formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for JAX HPC Sumner |
last update 2022-07-27formatting: passedlinting: failed |
0 |
0 |
||
This workflow performs a metatranscriptomics and bulk RNAseq analysis from the sequencing output dat… |
bioinformatics bulk-rna-seq conda-environment docker metatranscriptomics singularity slurm-cluster snakemake |
last update 2022-07-27formatting: failedlinting: failed |
0 |
1 |
|
Fosmid assembly annotation |
last update 2022-07-24formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2022-06-17formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-07-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-07-19formatting: failedlinting: failed |
0 |
3 |
||
test |
last update 2022-07-19formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-07-19formatting: failedlinting: failed |
0 |
1 |
||
ReMM score snakemake workflow |
last update 2022-07-19formatting: passedlinting: passed |
0 |
3 |
||
Mtb variant calling pipeline (bwa/GATK) |
last update 2022-10-13formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake workflow and associated scripts to make population genomic stat tracks for the UCSC Geno… |
last update 2021-03-03formatting: failedlinting: failed |
0 |
1 |
||
KAS-Seq Analysis Workflow |
last update 2021-03-03formatting: passedlinting: passed |
0 |
1 |
||
An example use of multiQC within snakemake |
last update 2021-03-01formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-02-26formatting: failedlinting: failed |
0 |
5 |
||
Analysis of RNA-seq data from Covid19 samples |
rna-seq rna-seq-pipeline |
last update 2021-02-26formatting: failedlinting: failed |
0 |
1 |
|
Repository detailing the analysis of a series of variants involved with boar taint |
last update 2021-02-23formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-02-22formatting: failedlinting: failed |
0 |
1 |
||
Tutorial to getting started with the Snakemake workflow manager |
last update 2021-02-18formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-02-18formatting: passedlinting: passed |
0 |
1 |
||
Week 7 of GGG 298 at UC Davis (Example Repository) |
last update 2021-06-24formatting: failedlinting: failed |
0 |
1 |
||
The main point of this assignment is for you to demonstrate your exploratory analysis skills and met… |
last update 2021-02-17formatting: failedlinting: failed |
0 |
1 |
||
RADSex paper analyses workflow |
workflow snakemake analyses |
last update 2021-02-19formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2021-02-16formatting: failedlinting: failed |
0 |
3 |
||
Snakemake implementation for quantifying mRNA, cRNA and vRNA of influenza virus |
last update 2022-03-08formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-07-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-07-18formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2022-10-26formatting: failedlinting: passed |
0 |
1 |
||
A workflow for the analysis of Lactobacillus plantarum. |
last update 2022-07-16formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-07-15formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2022-07-14formatting: failedlinting: failed |
0 |
1 |
||
DiVA (DNA Variant Analysis) is a pipeline for Next-Generation Sequencing Exome data anlysis |
bioinformatics snakemake genomics workflow variant-calling variant-annotations |
last update 2022-07-14formatting: failedlinting: failed |
0 |
5 |
|
No description available. |
last update 2022-07-13formatting: failedlinting: failed |
0 |
0 |
||
Workflow for analyzing SARS-CoV-2 spike RBD amplicon Illumina data. |
last update 2022-07-13formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2022-07-13formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2022-07-13formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2022-07-13formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2022-07-13formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2022-07-10formatting: failedlinting: failed |
0 |
1 |
||
Developing Read Abundance rule |
last update 2022-10-04formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2022-06-22formatting: failedlinting: passed |
0 |
2 |
||
No description available. |
last update 2022-07-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-06-10formatting: failedlinting: failed |
0 |
2 |
||
Snakemake workflow for BOLT-LMM based GWAS analyses |
last update 2022-07-07formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2022-06-20formatting: failedlinting: failed |
0 |
1 |
||
cap-tcr |
last update 2022-07-01formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2022-06-28formatting: passedlinting: passed |
0 |
1 |
||
snakemake workflow of circs : circRNA detection from RNASeq |
last update 2022-07-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-07-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-06-01formatting: failedlinting: failed |
0 |
1 |
||
This repository contains materials for snakemake and nexflow languages |
last update 2022-07-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-06-29formatting: failedlinting: failed |
0 |
0 |
||
A snakemake pipeline to trim primers and adaptors from illumina reads and also provides useful stat… |
last update 2022-06-29formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-06-09formatting: failedlinting: failed |
0 |
1 |
||
Downloads TCGA data and puts it into a nice HDF file |
last update 2022-01-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-05-16formatting: failedlinting: failed |
0 |
1 |
||
Design and selection of gRNAs for pooled CRISPRi tiling screens |
last update 2022-06-27formatting: failedlinting: failed |
0 |
6 |
||
Given a set of index, fastq and sample to barcode file, generate a directory structure with each sam… |
last update 2022-06-01formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-09-12formatting: failedlinting: failed |
0 |
1 |
||
UMI Barcoded Illumina 2x250 BCR mRNA Preprocessing with Presto |
last update 2022-02-11formatting: failedlinting: failed |
0 |
1 |
||
Identification of optimal sWGS bin size to model SNP6 arrays |
last update 2022-06-15formatting: failedlinting: failed |
0 |
4 |
||
Snakemake scRNAseq |
last update 2022-06-24formatting: failedlinting: passed |
0 |
1 |
||
Simple snakemake workflow for SNP calling, annotation and visualization. |
last update 2022-06-23formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for performing an RNA-seq analysis |
snakemake reproducible-research reproducible-science rna-seq rna-seq-pipeline |
last update 2022-06-22formatting: failedlinting: failed |
0 |
1 |
|
Snakemake workflow for downloading Ensembl reference genomes for use in downstream bioinformatics an… |
reference-genomes reproducible-research reproducible-science snakemake |
last update 2022-06-22formatting: failedlinting: failed |
0 |
1 |
|
Snakemake workflow to fetch, process and map reads to reference. |
last update 2022-06-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-06-09formatting: failedlinting: failed |
0 |
1 |
||
forked from official CADD repo, with added custom installation scripts and integration into the WiNG… |
last update 2022-06-21formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-06-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-06-18formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-04-13formatting: failedlinting: failed |
0 |
1 |
||
A workflow for getting information of genes based on RNA-seq data |
last update 2022-06-08formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-05-05formatting: failedlinting: failed |
0 |
1 |
||
Run MeDEStrand with bedpe input as part of PLBR database workflow |
last update 2022-04-25formatting: failedlinting: failed |
0 |
1 |
||
Run MedRemix with bedpe input as part of PLBR database workflow |
last update 2022-05-16formatting: failedlinting: failed |
0 |
1 |
||
A workflow to integrate gene attribute prediction tools into a single data matrix |
last update 2022-04-04formatting: failedlinting: failed |
0 |
1 |
||
Abstract & Poster for ASM Microbe 2022 |
last update 2022-06-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-06-06formatting: failedlinting: failed |
0 |
1 |
||
One-off analyses and figures for Bragdon et. al. 2022. |
last update 2022-06-05formatting: failedlinting: failed |
0 |
5 |
||
Workflow used to compare RNA-seq and ChIP-seq data for Bragdon et. al. 2022. |
last update 2022-06-05formatting: failedlinting: failed |
0 |
5 |
||
Snakemake pipeline for Upstream processing of scRNA-seq libraries generated by a customized Smartseq… |
last update 2022-02-17formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-05-31formatting: failedlinting: failed |
0 |
1 |
||
Creating alignment references in different coordinates |
last update 2022-06-10formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for shallow WGS analysis |
last update 2022-05-18formatting: failedlinting: failed |
0 |
0 |
||
RNA-seq analysis pipeline used in Bragdon et. al. 2022. |
last update 2022-06-05formatting: failedlinting: failed |
0 |
5 |
||
ChIP-seq analysis pipeline used in Bragdon et. al. 2022. |
last update 2022-06-05formatting: failedlinting: failed |
0 |
5 |
||
Snakemake workflow for processing Arima HIC data |
last update 2022-06-04formatting: failedlinting: failed |
0 |
1 |
||
Comparative and Evolutive Genomics SnakeMake Workflow |
last update 2022-05-20formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow to analyze the single-cell RNA-seq dataset of sea urchin |
last update 2022-05-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-02-24formatting: failedlinting: failed |
0 |
1 |
||
Genetic pipeline to detect variants from a genome of reference |
cnn-keras docker singularity |
last update 2022-06-02formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2022-02-03formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-04-26formatting: failedlinting: failed |
0 |
1 |
||
RNA-seq pipeline comparison and analyses |
last update 2022-04-02formatting: failedlinting: failed |
0 |
1 |
||
Testing out SnakeMake as a new tool for Benchtests |
last update 2022-01-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-05-03formatting: failedlinting: failed |
0 |
1 |
||
This workflow performs the identification of gene members of a particular gene family for a given sp… |
last update 2022-05-30formatting: failedlinting: failed |
0 |
1 |
||
Generating Controlled Vocabulary from C2M2 |
last update 2022-09-12formatting: failedlinting: failed |
0 |
2 |
||
Snakemake/Hydra workflow to analyse RNASeq data |
last update 2022-05-30formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2022-07-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-01-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-05-24formatting: failedlinting: failed |
0 |
1 |
||
snakemake workflow for WRF-Hydro postprocessing |
last update 2022-05-20formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake workflow to automate analysis of whole-genome bisulfite sequencing data. |
last update 2022-05-22formatting: failedlinting: failed |
0 |
1 |
||
Repository for m5c data analysis |
last update 2022-05-21formatting: failedlinting: failed |
0 |
2 |
||
A nimagen workflow implemented in snakemake. |
last update 2022-05-23formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2022-05-18formatting: failedlinting: failed |
0 |
3 |
||
Snakemake pipeline for running vina |
last update 2022-05-13formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-12-29formatting: failedlinting: failed |
0 |
1 |
||
WindSPORES reproducible workflow |
last update 2022-04-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-03-21formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-11-16formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-04-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-08-15formatting: failedlinting: failed |
0 |
1 |
||
Pipeline based on hydra modules for in-house validation of qiagen’s qiaseq bioinformatics pipeline |
last update 2022-05-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-03-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-05-10formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-05-09formatting: failedlinting: failed |
0 |
1 |
||
template building for cam-can dataset |
last update 2022-05-06formatting: failedlinting: failed |
0 |
3 |
||
snakemake workflow for computing binding energies of adsorbates using Quantum Espresso |
last update 2022-05-02formatting: failedlinting: failed |
0 |
1 |
||
Nevada-Bioinformatics-Center/snakemake_sanger_tracy_variants- |
No description available. |
last update 2022-05-05formatting: failedlinting: failed |
0 |
2 |
|
Exploring Bacillus subtilis pangenome in metagenomes |
last update 2022-05-05formatting: failedlinting: failed |
0 |
2 |
||
This pipeline contains the data processing steps used for Thuy Ngo’s 2019 cell-free RNA manuscript |
last update 2022-04-25formatting: failedlinting: failed |
0 |
4 |
||
No description available. |
last update 2022-05-03formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for StandardizedPlastidPhylogenomics |
last update 2022-05-02formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow to inject SNPs from a strain into a the mouse refrence genome and create a cellra… |
last update 2022-04-06formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-05-01formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-05-01formatting: failedlinting: failed |
0 |
1 |
||
Processing pipeline for single-cell barcoded Tn5 assays |
last update 2022-04-29formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2022-04-29formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-04-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-04-28formatting: failedlinting: passed |
0 |
1 |
||
This snakemake pipeline starts with a root directory and archives/compresses all subdirectories and … |
ceph pipeline rclone snakemake storage workflow shell |
last update 2022-06-14formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2022-04-28formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2022-04-28formatting: failedlinting: failed |
0 |
0 |
||
Quality assessment workflow for COVID-19 |
last update 2021-10-24formatting: failedlinting: failed |
0 |
4 |
||
This is a Snakemake workflow to filter repeat libraries for TEs resembling proteins |
last update 2022-04-22formatting: failedlinting: failed |
0 |
6 |
||
No description available. |
last update 2022-04-21formatting: failedlinting: failed |
0 |
1 |
||
A pipeline to detect aberrant RNA events for clinical diagnostics in rare disease |
last update 2021-10-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-04-14formatting: failedlinting: failed |
0 |
1 |
||
RNA-Seq, a snakemake pipeline for data analysis and data processing. |
last update 2022-04-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-04-14formatting: passedlinting: passed |
0 |
1 |
||
No description available. |
last update 2022-04-13formatting: failedlinting: failed |
0 |
1 |
||
Quick demo for Snakemake to present during the Hacky Hour at DPG spring meeting in Erlangen 2022. |
last update 2022-03-14formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-04-12formatting: passedlinting: passed |
0 |
1 |
||
workflowr for contributions to EB-QTL project |
last update 2022-02-02formatting: failedlinting: failed |
0 |
1 |
||
Integrative Pipeline for Splicing Analysis |
last update 2022-04-08formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-05-19formatting: failedlinting: failed |
0 |
1 |
||
An ensemble variant calling pipeline handling either DNA or RNA seq datasets. |
last update 2022-02-21formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-06-15formatting: failedlinting: failed |
0 |
3 |
||
Lecture on Social Media Landscape @ SMWA |
last update 2022-04-01formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2022-04-01formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2021-11-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-03-31formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2022-03-31formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-03-31formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-03-31formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-03-31formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-03-31formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-03-31formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-03-30formatting: failedlinting: failed |
0 |
1 |
||
A light weight pipeline for RNA-seq analysis. Orignally design for cell free RNA-seq data analysis,… |
last update 2021-12-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-12-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-03-29formatting: failedlinting: failed |
0 |
1 |
||
Dummy snakemake workflow to use as input to another workflow |
last update 2022-03-29formatting: failedlinting: failed |
0 |
1 |
||
Pipeline used to analyze RNA-Seq data from a new La protein pulldown of RNA in Tetrahymena thermophi… |
last update 2022-03-25formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for generating read count data from CRISPR screens. |
last update 2021-12-19formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline to detect miRNA |
mirna |
last update 2022-03-28formatting: failedlinting: failed |
0 |
1 |
|
Workflow to get hhsuite works from conda and fasta alignments |
last update 2022-03-11formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline to detect novel lncRNA |
lncrna |
last update 2022-03-28formatting: failedlinting: failed |
0 |
1 |
|
Datasets accompanying MALVIRUS |
last update 2021-11-16formatting: failedlinting: failed |
0 |
8 |
||
Variant calling pipeline (Snakemake workflow) |
bioinformatics pipeline ngs-analysis variant-calling |
last update 2022-04-01formatting: failedlinting: failed |
0 |
1 |
|
snaktest |
last update 2022-03-27formatting: failedlinting: failed |
0 |
1 |
||
The repository host the snakemake file for 16S rRNA and shotgun sequencing data including QIIME2 and… |
last update 2022-03-26formatting: failedlinting: failed |
0 |
1 |
||
DNAscan2 is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Ge… |
last update 2022-05-06formatting: failedlinting: failed |
0 |
2 |
||
Pipeline implementing the MERIDA logical modelling method using Snakemake to dispatch hyperparmeter … |
last update 2021-12-14formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2022-03-21formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for metagenomics analysis using QIIME 2 as its core |
last update 2022-03-21formatting: failedlinting: failed |
0 |
1 |
||
Virome taxonomic profiling using BLAST |
last update 2022-03-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-03-21formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-10-13formatting: failedlinting: failed |
0 |
1 |
||
WES analysis pipeline |
last update 2022-03-17formatting: failedlinting: failed |
0 |
1 |
||
Snakemake tutorial |
last update 2022-03-08formatting: passedlinting: passed |
0 |
1 |
||
runs trimming, bowtie2 and QC. |
last update 2022-03-22formatting: failedlinting: failed |
0 |
2 |
||
Example of combining multiple Snakemake files as modules |
last update 2022-03-03formatting: passedlinting: failed |
0 |
1 |
||
A pipeline for QC |
last update 2022-02-26formatting: failedlinting: failed |
0 |
3 |
||
Calling local ancestry tracts with RFMix v1.5.4 and (optionally) validating global ancestry fraction… |
last update 2022-03-13formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2022-03-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-03-11formatting: failedlinting: failed |
0 |
1 |
||
Pipeline to run qiime2 with snakemake |
last update 2022-02-01formatting: failedlinting: failed |
0 |
0 |
||
Code For Mental Health - Hackathon #bitsxlaMarató 2021 |
last update 2022-03-02formatting: failedlinting: failed |
0 |
1 |
||
Data and code associated with the upcoming manuscript on killifish microbiota |
last update 2021-12-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-02-12formatting: failedlinting: failed |
0 |
3 |
||
Pipeline to map short reads from several samples to a reference genome |
pipelines bioinformatics bioinformatics-pipeline snakemake-pipeline mapping |
last update 2022-02-21formatting: failedlinting: failed |
0 |
1 |
|
snakemake-workflow for SARS-CoV2 reads generate with Nanopore+Artic for later integration into UnCoV… |
last update 2022-01-10formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-03-01formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-03-01formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-01-03formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-02-07formatting: failedlinting: failed |
0 |
1 |
||
Short read mapping and variant calling |
pipeline snakemake snakemake-pipeline short-reads mapping freebayes variant-calling |
last update 2021-11-22formatting: failedlinting: failed |
0 |
1 |
|
Snakemake pipeline for phylogenetic placement of metagenomic sequences |
last update 2022-03-01formatting: failedlinting: failed |
0 |
3 |
||
A proteogenomics approach to identify cancer variants and neoantigens |
last update 2022-02-24formatting: failedlinting: failed |
0 |
1 |
||
Automate screening for CRISPR-Cas and MGEs ✂️🧬 |
last update 2022-01-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-02-25formatting: failedlinting: failed |
0 |
1 |
||
degree project, predict patient outcome with RNA-seq data |
last update 2022-02-22formatting: failedlinting: failed |
0 |
1 |
||
A pipeline for processing RNA-seq data using Snakemake and HISAT2. |
last update 2022-02-17formatting: passedlinting: passed |
0 |
1 |
||
APA target caller - derived from the exar2020 paper |
last update 2021-12-09formatting: failedlinting: failed |
0 |
2 |
||
Workflow to automate reference file acquisition and preparation for analysis pipelines |
last update 2022-02-15formatting: passedlinting: failed |
0 |
3 |
||
Snakemake pipeline for ATAC-Seq |
atac-seq snakemake |
last update 2022-02-01formatting: failedlinting: failed |
0 |
1 |
|
Snakemake pipeline to generate multiscale methylation plots |
last update 2022-02-17formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2022-02-17formatting: failedlinting: failed |
0 |
0 |
||
pipeline to perform gbs and genetic fitness analysis |
gbs scaffolding bioinformatics pipeline snakemake snakemake-pipeline genotyping-by-sequencing |
last update 2021-11-04formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2022-02-15formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-01-10formatting: passedlinting: passed |
0 |
3 |
||
Snakemake decoupleR wrapper |
last update 2022-01-03formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-05-10formatting: failedlinting: failed |
0 |
5 |
||
No description available. |
last update 2022-01-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-02-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-02-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-02-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-02-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-02-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-02-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-02-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-02-07formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for processing Micro-C data |
last update 2022-02-04formatting: failedlinting: failed |
0 |
1 |
||
explore snakemake configs |
last update 2021-12-06formatting: failedlinting: failed |
0 |
1 |
||
marmoset template building WIP |
last update 2022-01-29formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-01-31formatting: failedlinting: failed |
0 |
1 |
||
Final semester project at the Bioinformatics institute. |
population-evolution |
last update 2022-05-21formatting: failedlinting: failed |
0 |
1 |
|
A next-generation sequencing assay designed to cover 179 cancer-associated genes |
last update 2022-01-30formatting: failedlinting: failed |
0 |
1 |
||
Metagenomics pipeline to find Relative Species Abundance |
last update 2022-01-10formatting: failedlinting: failed |
0 |
1 |
||
Example algorithm comparison workflow |
last update 2022-01-15formatting: failedlinting: failed |
0 |
2 |
||
Post-acquisition processing pipelines for light-sheet microscopy |
last update 2022-01-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-03-28formatting: failedlinting: failed |
0 |
1 |
||
GATK variant calling for RNASeq |
gatk rnaseq variant calling |
last update 2022-02-18formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2022-01-20formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow to run pangolin on all SARS-CoV-2 sequences in ENA |
last update 2021-12-17formatting: failedlinting: failed |
0 |
1 |
||
Pipeline for detecting recurrent sequence evolution between pairs of duplicated genes |
last update 2022-01-20formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for Gene Set Enrichment: pathway and GO enrichment analysis |
go pathway |
last update 2022-03-28formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2022-01-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-01-14formatting: failedlinting: failed |
0 |
1 |
||
Sourmash snakemake workflow for quick isolate genome scanning |
last update 2022-01-12formatting: failedlinting: failed |
0 |
1 |
||
Snakemake implementation of the uniclust pipeline |
last update 2022-01-14formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-01-13formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline to perform reference based transcriptomics |
last update 2022-01-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-01-07formatting: failedlinting: failed |
0 |
6 |
||
Example of how to script figure creation with inkscape and python |
last update 2022-01-06formatting: failedlinting: failed |
0 |
1 |
||
Tobacco Hornworm as a novel host model for the study of fungal virulence and drug efficacy |
last update 2022-01-05formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-01-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-12-29formatting: failedlinting: failed |
0 |
1 |
||
Snakemake Workflow of Master’s Thesis |
bioinformatics metagenomics |
last update 2021-12-26formatting: failedlinting: failed |
0 |
1 |
|
Snakemake version of purge_tips |
last update 2021-12-24formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake workflow for visualising UK Covid-19 data |
last update 2021-12-21formatting: passedlinting: passed |
0 |
1 |
||
genome tRNA annotation |
last update 2021-12-20formatting: failedlinting: failed |
0 |
1 |
||
Phylogeography of SARS-CoV-2 |
last update 2021-12-19formatting: failedlinting: failed |
0 |
1 |
||
Build resitance gene catelogue based the RGI output from CARD, and do alignements (packed in the Sna… |
last update 2021-12-17formatting: failedlinting: failed |
0 |
1 |
||
miRNA analysis pipeline |
last update 2021-12-17formatting: failedlinting: failed |
0 |
3 |
||
General snakemake pipeline to generate cell matrices for single-cell analysis and .loom files to ass… |
last update 2021-12-14formatting: failedlinting: failed |
0 |
1 |
||
Clinical Genomics Uppsala inheritance disease pipeline for WGS |
last update 2022-02-14formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-12-13formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2021-12-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-12-13formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2021-12-12formatting: failedlinting: failed |
0 |
1 |
||
snakemake pipeline for DNA mapping and coverage stats |
last update 2021-12-11formatting: failedlinting: failed |
0 |
1 |
||
CHROME ChIPseq analysis associated with GEO: GSE190413 |
last update 2021-12-09formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for calling somatic mtDNA single nucleotide variants, used in Passman et al 2021 |
last update 2021-12-09formatting: failedlinting: failed |
0 |
1 |
||
Code to setup and maintain reference assemblies and accompanying data |
last update 2021-08-12formatting: failedlinting: failed |
0 |
4 |
||
Snakemake workflow for making synthetic tumours |
bioinformatics cancer-genomics sequencing genomics |
last update 2021-12-08formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2021-12-07formatting: failedlinting: failed |
0 |
2 |
||
A small example to test DENTIST’s workflow |
snakemake singularity workflow dentist docker pacbio genome-assembly long-reads gap-filling |
last update 2021-12-06formatting: failedlinting: failed |
0 |
2 |
|
Re-mapping of Granja et al. (2019) scATAC-seq data to hg38 |
last update 2021-12-06formatting: failedlinting: failed |
0 |
1 |
||
Reproduction of Leiby et al. placental microbiome paper |
last update 2022-02-15formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-12-03formatting: failedlinting: failed |
0 |
1 |
||
Data integration and build pipeline for EpiGraphDB Neo4j graph |
last update 2021-05-04formatting: failedlinting: failed |
0 |
11 |
||
No description available. |
last update 2021-12-03formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2022-02-10formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-12-03formatting: failedlinting: failed |
0 |
1 |
||
WGS workflow to generate results for the ALL2Gether protocol |
last update 2021-12-01formatting: failedlinting: failed |
0 |
1 |
||
workflow for hifiasm assembly stuff |
last update 2021-12-01formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-11-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-11-30formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-11-28formatting: failedlinting: failed |
0 |
1 |
||
Hello, World! example for Snakemake |
last update 2021-11-28formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for Upstream processing of Smartseq2 sequenced libraries |
last update 2021-11-26formatting: failedlinting: failed |
0 |
0 |
||
Snakemake workflow for running BIDS App pre-processing on EpLink data |
last update 2021-11-25formatting: failedlinting: failed |
0 |
1 |
||
A pipeline to identify sites of positive selection in viral genomes using the FUBAR algorithm. |
last update 2021-11-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-11-01formatting: failedlinting: failed |
0 |
1 |
||
Demo Snakemake workflow - small and runs quickly for testing purposes. |
snakemake genomics |
last update 2021-11-24formatting: failedlinting: failed |
0 |
1 |
|
This a snakemake pipeline to detect Somatic mutations from RNASeq. |
last update 2021-11-29formatting: failedlinting: failed |
0 |
0 |
||
Simple workflow to map WGS data to reference genome according to GATK best practices |
last update 2021-08-18formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake tutorial workflow using the recent ABRF beer proteomics study. |
last update 2021-11-18formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-11-18formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for pre-processing dwi data to re-train using b1000 hcp data |
last update 2021-11-16formatting: failedlinting: failed |
0 |
2 |
||
pipeline for HTAN bulk RNA-Seq data quantification |
last update 2021-11-15formatting: failedlinting: failed |
0 |
21 |
||
SNAKEMAKE WF ATACSEQ |
snakemake |
last update 2021-11-15formatting: failedlinting: failed |
0 |
1 |
|
A Snakemake workflow for encrypting files before uploading them to the Swedish node of the European … |
last update 2021-11-15formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-11-14formatting: failedlinting: passed |
0 |
3 |
||
No description available. |
last update 2021-11-15formatting: failedlinting: failed |
0 |
1 |
||
Analysis of constructs from the ECLS-K:2011 with the Measurement Model of Derivatives (MMOD; Estabro… |
last update 2021-11-11formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for Greedy template generation on developing HCP data |
last update 2021-11-10formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake workflow to extract PGx information from WES data. |
last update 2021-11-10formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-11-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-11-08formatting: failedlinting: failed |
0 |
1 |
||
This is the template from the bodenmiller readme |
last update 2021-11-05formatting: failedlinting: failed |
0 |
1 |
||
Getting started with Snakemake workflows for automated bioinformatics analysis. |
last update 2021-11-05formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2021-11-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-11-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-11-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-11-01formatting: failedlinting: failed |
0 |
1 |
||
Pipeline to extract protein domain clusters from sequence data |
last update 2021-10-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-10-25formatting: failedlinting: failed |
0 |
1 |
||
A snakemake pipeline improves the gene annotation for cross species analysis of single cell RNA-Seq |
last update 2021-10-25formatting: failedlinting: failed |
0 |
3 |
||
Build a phylogeny with FastTree based on a concatenated alignment of 103 marker genes identified wit… |
last update 2021-10-22formatting: failedlinting: failed |
0 |
1 |
||
Uses |
snakemake bismark slurm |
last update 2021-10-22formatting: failedlinting: failed |
0 |
2 |
|
No description available. |
last update 2021-10-21formatting: failedlinting: failed |
0 |
2 |
||
workflow for processing ISMRM Diffusion Study - Best Practices in Image Preprocessing data |
last update 2021-10-20formatting: failedlinting: failed |
0 |
1 |
||
Repository containing a Snakemake ChIPseq pipeline for SE and PE datasets |
last update 2021-10-20formatting: failedlinting: failed |
0 |
1 |
||
bioinformatics tutorial demonstrating a simple workflow for cDNA based differential gene expression … |
last update 2021-10-20formatting: failedlinting: failed |
0 |
0 |
||
Snakemake workflow for non-model organism analyses |
last update 2021-10-19formatting: failedlinting: passed |
0 |
37 |
||
RNA seq workflow by snakemake |
last update 2021-10-18formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-10-17formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-10-16formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-10-15formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-10-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-10-29formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-10-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-10-11formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for gene prediction usinh snakemake |
last update 2021-10-08formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-10-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-10-04formatting: failedlinting: failed |
0 |
1 |
||
Creating a snakemake workflow for mapping the modern data, filtering, genotype calling and then filt… |
last update 2021-10-04formatting: failedlinting: failed |
0 |
1 |
||
Quantify HERVs in single-cell sequencing data |
last update 2021-09-30formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for generating gene expression counts from RNA-sequencing data. |
last update 2021-11-01formatting: failedlinting: failed |
0 |
1 |
||
A human-first SV annotation snakemake pipeline based on nanotatoR working with optical mapping (Bion… |
bionano optical structural-variation genome-analysis smap r annotation |
last update 2021-09-30formatting: failedlinting: failed |
0 |
0 |
|
No description available. |
last update 2021-09-29formatting: failedlinting: failed |
0 |
1 |
||
Template for a new project |
last update 2021-09-29formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-09-28formatting: failedlinting: failed |
0 |
1 |
||
data from national cancer institute for cancer research |
last update 2021-09-28formatting: failedlinting: failed |
0 |
1 |
||
Single cell data from the EBV-transformed lymphoblastoid cell line paper |
last update 2021-09-27formatting: failedlinting: failed |
0 |
1 |
||
Quantify HERVs in Tabula Sapiens datasets using single-cell Telescope (scTelescope) |
last update 2021-09-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-12-17formatting: failedlinting: failed |
0 |
2 |
||
A workflow to run PING (Pushing Immunogenetics to the Next Generation) efficiently on NIH Biowulf |
last update 2021-09-24formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2021-09-23formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-11-10formatting: failedlinting: failed |
0 |
1 |
||
Tools for exploring GWAS / QTL colocalization results |
last update 2021-09-23formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for calling CNAs from Affymetrix (now Thermofisher) Cytoscan and Oncoscan arrays |
last update 2021-09-25formatting: failedlinting: failed |
0 |
3 |
||
Simple pipeline to retrieve a DNA sequences, fold them with LinearFold, and vizualise them with forg… |
last update 2021-09-17formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-09-17formatting: failedlinting: failed |
0 |
2 |
||
Metagenomic pipeline managed by snakemake |
last update 2021-09-14formatting: failedlinting: failed |
0 |
0 |
||
A Snakemake Workflow for analysis of Cancer RNASeq data |
last update 2021-09-13formatting: failedlinting: failed |
0 |
1 |
||
A snakemake workflow for RNASeq data using STAR and trimmomatic to process SE read data |
last update 2021-09-10formatting: failedlinting: failed |
0 |
3 |
||
A workflow to automate the annotation of newick trees for COVID-19 |
last update 2021-09-10formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-09-08formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-11-03formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-09-08formatting: failedlinting: failed |
0 |
1 |
||
Attempting to impute and phase low coverage sequencing data in Anopheles |
last update 2021-09-07formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for the analysis of retrotransposition in Dictyostelium discoideum. |
last update 2021-09-07formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-09-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-09-01formatting: failedlinting: failed |
0 |
5 |
||
No description available. |
last update 2021-08-31formatting: failedlinting: failed |
0 |
1 |
||
Simulate integrations and score results |
last update 2021-11-29formatting: failedlinting: failed |
0 |
2 |
||
snakemake workflow for mappind single/paired datas |
last update 2021-11-04formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2021-10-21formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2021-09-17formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-09-05formatting: failedlinting: failed |
0 |
1 |
||
Covid Illumina sequence data processing pipeline |
last update 2021-08-31formatting: failedlinting: failed |
0 |
2 |
||
Snakemake workflow for calling somatic variants in tumors |
last update 2021-08-26formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow that runs trimmomatic for trimming, and STAR and/or HISAT2 for aligning. |
last update 2021-08-23formatting: failedlinting: failed |
0 |
1 |
||
Snakemake project for common mm10 reference files |
last update 2021-08-20formatting: failedlinting: failed |
0 |
1 |
||
Workflow to call structural and copy number variants in somatic whole genome data |
last update 2021-08-19formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-08-18formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2021-08-18formatting: passedlinting: failed |
0 |
1 |
||
A basic Snakemake template repo |
last update 2021-08-18formatting: failedlinting: failed |
0 |
2 |
||
Create panel of normals for different tools |
last update 2021-08-17formatting: passedlinting: failed |
0 |
1 |
||
GeneMANIA data processing pipeline |
last update 2021-08-16formatting: failedlinting: failed |
0 |
8 |
||
No description available. |
last update 2021-08-16formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-08-13formatting: failedlinting: failed |
0 |
4 |
||
The repo used to compare several kinds of tools used to detect alternative splicing. |
last update 2021-08-13formatting: failedlinting: failed |
0 |
1 |
||
Installing and using DESeq2 to analyzed ONT cDNA data |
last update 2021-08-10formatting: failedlinting: failed |
0 |
1 |
||
Benchmarking single-cell DNA variant calling |
last update 2021-08-10formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2021-08-07formatting: failedlinting: failed |
0 |
1 |
||
Simulation of Related, MDA Amplified Single Cells |
last update 2021-08-06formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for slamDunk toolkit |
last update 2021-08-05formatting: failedlinting: passed |
0 |
1 |
||
A pipeline for identification and annotation of transposable element (TE) insertions using next gene… |
ngs fastq gene transposable-elements mobile-genetic-elements gene-annotation |
last update 2021-08-05formatting: failedlinting: failed |
0 |
1 |
|
Internship project with Medinsights |
last update 2021-08-04formatting: failedlinting: failed |
0 |
1 |
||
Trade-off between land use and cost of renewable electricity in Europe. |
last update 2021-08-04formatting: failedlinting: failed |
0 |
1 |
||
Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://… |
ncats-translator |
last update 2021-08-03formatting: failedlinting: failed |
0 |
4 |
|
No description available. |
last update 2021-08-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-08-01formatting: passedlinting: passed |
0 |
1 |
||
Analysis of 16S sequencing data via |
last update 2021-07-31formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for running ancestry-specific IBDNe |
last update 2021-07-30formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-07-30formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2021-07-30formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-07-29formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-07-28formatting: failedlinting: failed |
0 |
1 |
||
Snakemake for demultiplexing 16S sequencing files using QIIME1 on the cluster. |
last update 2021-07-24formatting: failedlinting: failed |
0 |
1 |
||
Tract-weighted functional connectivity snakemake workflow - WIP |
last update 2021-07-23formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for generating DrEdGE single cell data |
last update 2021-07-23formatting: failedlinting: failed |
0 |
2 |
||
A Snakemake pipeline to call variants (SNPs, InDels) from DNA-seq Illumina fastq files. |
last update 2021-07-21formatting: failedlinting: failed |
0 |
3 |
||
Comparative genomics between Varroa destructor and Varroa jacobsoni to identify genetic mechanisms a… |
last update 2021-07-21formatting: failedlinting: failed |
0 |
2 |
||
Reproducible code for workflow and evaluations in our paper evaluating genetic variation-based demul… |
last update 2021-07-20formatting: failedlinting: failed |
0 |
1 |
||
Code for the analyses from the review Metabolic landscapes in sarcomas |
last update 2021-07-14formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-07-09formatting: failedlinting: failed |
0 |
3 |
||
TCR sequencing and analysis with MiXCR and Immunarch |
last update 2021-07-09formatting: failedlinting: failed |
0 |
1 |
||
RNA-seq alignment and DESeq2 Analysis |
last update 2021-07-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-07-08formatting: failedlinting: failed |
0 |
5 |
||
No description available. |
last update 2021-07-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-07-06formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-07-06formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow to grab raw fastqs from SRA from SRR, SRX, SRP, or PJRNA accession numbers |
last update 2021-06-30formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-06-30formatting: failedlinting: failed |
0 |
1 |
||
Scripts used for handling my E coli assemblies collection |
last update 2021-06-30formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-06-29formatting: failedlinting: failed |
0 |
1 |
||
Implementation of the tumor only version of the GOAL Consortium Consensus Pipeline in Snakemake |
last update 2021-06-29formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-06-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-06-24formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2021-06-23formatting: failedlinting: failed |
0 |
1 |
||
Reference-free, sequence composition-based engraftment analysis of metagenomes from the FECBUD study |
last update 2021-06-23formatting: failedlinting: failed |
0 |
1 |
||
Benchmarking bwamem on slurm cluster |
last update 2021-06-23formatting: passedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-06-22formatting: passedlinting: failed |
0 |
1 |
||
Non Invasive Analysis of Somatic Mutations in Cancer |
last update 2021-06-18formatting: failedlinting: failed |
0 |
1 |
||
Code for topology-based approximations for N-1 contingency constraints |
last update 2021-06-18formatting: failedlinting: failed |
0 |
3 |
||
Snakemake workflow for executing GATK-SV Module00a on a local HPC facility via Slurm |
last update 2021-06-17formatting: failedlinting: failed |
0 |
2 |
||
A newerer and betterer pipelord version featuring wrappers |
last update 2021-06-16formatting: failedlinting: failed |
0 |
1 |
||
Evaluate de novo motif finding tools |
last update 2021-06-14formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-06-14formatting: failedlinting: failed |
0 |
1 |
||
Celluloid: clustering single cell sequencing data around centroids |
last update 2021-06-13formatting: failedlinting: failed |
0 |
7 |
||
No description available. |
last update 2021-06-12formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2021-06-12formatting: failedlinting: failed |
0 |
1 |
||
Snakemake2 |
last update 2021-06-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-06-04formatting: failedlinting: failed |
0 |
1 |
||
Analysis of mutational antigenic profiling of SARS-CoV-2 RBD against monoclonal antibodies and conva… |
last update 2021-06-03formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2021-06-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-06-02formatting: failedlinting: failed |
0 |
1 |
||
Lecture 7 of Social Media and Web Analytics |
last update 2021-06-01formatting: failedlinting: failed |
0 |
1 |
||
Code to analyze targetted BS-seq data in collaboration with Parker and Marra et al. |
last update 2021-06-01formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2021-05-30formatting: failedlinting: failed |
0 |
1 |
||
Processing sorted cells from BC1 that have been bulkrnaseq’d |
last update 2021-05-28formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for shallow WGS analysis |
last update 2021-05-31formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2021-05-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-05-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-05-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-05-27formatting: failedlinting: failed |
0 |
2 |
||
Snakemake workflow for downloading HCP Lifespan data |
last update 2021-05-27formatting: failedlinting: failed |
0 |
1 |
||
Benchmarking and assembly |
last update 2021-05-27formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2021-05-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-05-25formatting: failedlinting: failed |
0 |
1 |
||
Learning about scRNA-Seq analysis using Snakemake. |
last update 2021-05-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-05-24formatting: failedlinting: failed |
0 |
1 |
||
SnakeMake workflow to retrieve viral contigs from bulk metagenomes |
last update 2021-05-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-05-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-05-17formatting: failedlinting: failed |
0 |
1 |
||
Mutational antigenic profiling of COV2-2196 and COV2-2130 |
last update 2021-05-17formatting: failedlinting: failed |
0 |
2 |
||
Lecture 5 of Social Media and Web Analytics |
last update 2021-05-16formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-02-10formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow to find 16S amplicons in bacterial genomes |
last update 2021-05-14formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-05-11formatting: failedlinting: failed |
0 |
1 |
||
Automated RNA-seq analysis pipeline using Snakemake |
last update 2021-05-11formatting: failedlinting: failed |
0 |
1 |
||
a snakemake workflow for rnaseq using hisat2 |
last update 2021-04-28formatting: failedlinting: failed |
0 |
1 |
||
Lecture 4 of social media and web analytics |
last update 2021-05-11formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-05-07formatting: failedlinting: failed |
0 |
2 |
||
Additional Training materials for workflows and package management |
last update 2019-07-16formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2021-02-17formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow implementing Accel Amplicon (Swift) trimming guidelines. |
last update 2018-11-23formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-08-28formatting: failedlinting: failed |
0 |
1 |
||
Reproduce PROBer paper analysis |
last update 2019-10-25formatting: failedlinting: failed |
0 |
5 |
||
Snakemake workflow for building an ANTS template (from antsMultivariateTemplateConstruction2.sh) |
last update 2020-09-30formatting: failedlinting: failed |
0 |
1 |
||
machine learning project for Cyber Carpentry 2019 |
last update 2019-07-26formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake workflow for characterizing and organizing microbial isolate genome sequences |
last update 2020-08-12formatting: failedlinting: failed |
0 |
1 |
||
pipeline i used for calling sQTL in chimps |
last update 2019-10-21formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2018-09-10formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2021-01-29formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
workflow dna ngs |
last update 2020-09-24formatting: failedlinting: failed |
0 |
2 |
|
This is a pipeline to run basic Chromatin immunoprecipitation sequencing analysis for single-end or … |
last update 2019-08-16formatting: failedlinting: failed |
0 |
0 |
||
This is a pipeline to run basic RNA-seq analysis for single-end data. |
last update 2020-02-27formatting: failedlinting: failed |
0 |
2 |
||
Pipeline for the analysis of Single-end ChIP-seq data |
last update 2018-11-22formatting: failedlinting: failed |
0 |
1 |
||
Data processing and analytics code for project Biodiversity and ecosystem services trade-offs |
last update 2017-06-12formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2020-06-19formatting: failedlinting: failed |
0 |
1 |
||
A snakemake workflow for an sRNA-seq data analysis pipeline developed by the Mosher Lab |
last update 2020-04-14formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2020-06-19formatting: failedlinting: failed |
0 |
1 |
||
Infer network from count data within Snakemake using a sparse Poisson lognormal model (PLNnetwork) |
snakemake snakemake-workflows microbiome-analysis network-inference count-data |
last update 2020-11-19formatting: failedlinting: failed |
0 |
1 |
|
LodSeq performs the genetic linkage analysis across families, by computing lod-scores given a gvcf f… |
genetic-linkage-analysis |
last update 2019-03-17formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2021-03-05formatting: passedlinting: passed |
0 |
1 |
||
A snakemake workflow for GWAS. |
last update 2019-12-03formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-07-31formatting: failedlinting: failed |
0 |
2 |
||
This workflow performs CLIP peak calling using omniCLIP. |
last update 2020-07-24formatting: failedlinting: failed |
0 |
1 |
||
Test usage of renv in a Snakemake pipeline |
last update 2020-07-05formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for running cellphonedb. |
last update 2020-11-23formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-06-15formatting: failedlinting: failed |
0 |
1 |
||
align and deduplicate paired reads from MPE-seq protocol |
last update 2019-08-21formatting: failedlinting: failed |
0 |
1 |
||
workflow-rymo1354 created by GitHub Classroom |
last update 2019-11-21formatting: failedlinting: failed |
0 |
2 |
||
Snakemake pipeline running |
last update 2020-07-15formatting: failedlinting: failed |
0 |
1 |
||
Snakemake example |
last update 2020-09-09formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for 10X using salmon alevin |
last update 2020-07-10formatting: failedlinting: failed |
0 |
1 |
||
Snakemake example workflow with singularity |
last update 2020-01-07formatting: failedlinting: failed |
0 |
1 |
||
Template snakemake pipeline for minimal tests |
last update 2020-08-26formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for quantitation of single-cell data using salmon alevin |
last update 2021-04-30formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for 10X using cellranger count |
last update 2021-04-30formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow to evaluate peak calling |
last update 2020-10-22formatting: failedlinting: failed |
0 |
1 |
||
Detect circRNAs in fastq files using CIRCExplorer and CIRI2 |
last update 2021-03-18formatting: failedlinting: failed |
0 |
0 |
||
Genome assembly evaluation workflow |
last update 2020-11-16formatting: failedlinting: passed |
0 |
1 |
||
Template repository for snakemake neuroimaging workflows |
last update 2020-07-29formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline to generate a reference index for Salmon Alevin |
last update 2020-07-23formatting: failedlinting: failed |
0 |
0 |
||
Pipeline for processing functional data of the 7T MELAS study |
last update 2021-04-30formatting: failedlinting: failed |
0 |
0 |
||
Demonstration Snakemake workflow for Ronin/AWS Slurm-based auto-scaling cluster |
snakemake ronin aws aws-parallelcluster |
last update 2020-05-04formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2021-05-05formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for structural connectome using mrtrix3 (loading BIDS data from prepdwi, fmriprep… |
last update 2020-04-24formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-01-09formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2021-03-11formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2021-05-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2019-10-08formatting: failedlinting: failed |
0 |
1 |
||
Benchmark of methods for 10X single-cell RNA-sequencing |
last update 2020-07-10formatting: failedlinting: failed |
0 |
1 |
||
tweaking chipseq workflow for ATACseq |
last update 2020-10-20formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2021-04-16formatting: failedlinting: failed |
0 |
1 |
||
test snakemake workflow |
last update 2021-01-15formatting: failedlinting: passed |
0 |
1 |
||
Clinical Analyis Pipeline - Snakemake |
last update 2018-12-03formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-05-08formatting: failedlinting: failed |
0 |
1 |
||
Experimental workflow for ATAC-seq data analysis using snakemake |
last update 2019-01-03formatting: failedlinting: failed |
0 |
1 |
||
A Snakemake workflow for the analysis of bacterial WGS data |
last update 2020-06-10formatting: failedlinting: failed |
0 |
2 |
||
CODA microbiome-analysis using aldex2, pylofactorisation |
last update 2021-04-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2018-06-19formatting: failedlinting: failed |
0 |
1 |
||
computes all variants including indels from Illumina sequences compared to a reference sequence |
last update 2019-09-11formatting: failedlinting: failed |
0 |
3 |
||
Snakemake workflow for RNA-seq mapping |
last update 2020-10-08formatting: failedlinting: passed |
0 |
1 |
||
Snakemake workflow for Kaiju analysis |
last update 2019-02-12formatting: failedlinting: failed |
0 |
1 |
||
The evaluation of MERFISHtools and the underyling model as published in the corresponding article. |
snakemake workflow snakemake-workflows |
last update 2018-06-15formatting: failedlinting: failed |
0 |
2 |
|
No description available. |
last update 2020-08-22formatting: failedlinting: failed |
0 |
2 |
||
A workflow for ChIP-seq analyses in Snakemake |
last update 2021-02-08formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-02-14formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2019-02-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-01-14formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2019-08-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2018-07-20formatting: failedlinting: failed |
0 |
1 |
||
running leaf cutter from snaptron data to identify differential splice events, esp those associate w… |
last update 2019-05-30formatting: failedlinting: failed |
0 |
0 |
||
A DNA sequencing pipeline based on the GATK best-practices workflow. |
last update 2019-07-25formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2020-05-08formatting: failedlinting: failed |
0 |
3 |
||
xander assembly pipeline to generate OTU and taxonomy table |
last update 2018-09-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-03-15formatting: failedlinting: failed |
0 |
1 |
||
rplB/rpsC targeted analyses with shotgun metagenomes |
rplb rpsc metagenome assembly diversity |
last update 2018-09-28formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
atac-seq snakemake single-cell |
last update 2018-07-13formatting: failedlinting: failed |
0 |
1 |
|
An RNASeq snakemake workflow using the Tuxedo suite. |
rnaseq-tuxedo rnaseq-pipeline rna-seq-pipeline rna-seq-snakemake snakemake snakemake-workflow |
last update 2019-07-24formatting: failedlinting: failed |
0 |
2 |
|
test |
last update 2019-01-28formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2021-03-26formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2020-12-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-12-18formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-04-27formatting: failedlinting: failed |
0 |
2 |
||
This Snakemake pipeline implements the GATK best-practices workflow for calling small germline varia… |
last update 2021-04-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-11-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-10-28formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-12-06formatting: failedlinting: failed |
0 |
1 |
||
Pipeline to process amplicon bisulfite sequencing results |
last update 2020-03-19formatting: failedlinting: failed |
0 |
0 |
||
GATK best-practiced Snakemake variant calling pipeline |
last update 2021-04-01formatting: passedlinting: passed |
0 |
1 |
||
No description available. |
last update 2019-07-23formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2020-10-19formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-05-02formatting: failedlinting: failed |
0 |
1 |
||
This repository contains the evalutation workflow used for the Segment Length Distribution chapter o… |
last update 2021-01-18formatting: failedlinting: failed |
0 |
1 |
||
Analysis of 4sU RNA-Seq data and calculation of rates using the INSPEcT package |
last update 2019-12-19formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2021-02-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-11-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-10-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2019-10-02formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2019-05-16formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-02-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-02-15formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-02-05formatting: passedlinting: passed |
0 |
1 |
||
No description available. |
last update 2021-04-09formatting: passedlinting: passed |
0 |
1 |
||
RNA-seq analysis snakemake pipeline with Kallisto and Sleuth |
last update 2019-10-08formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-01-19formatting: passedlinting: passed |
0 |
1 |
||
No description available. |
last update 2020-09-10formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-06-16formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-10-19formatting: failedlinting: failed |
0 |
1 |
||
pipeline to find unique primer for genome bins in metagenomes |
last update 2018-11-07formatting: failedlinting: failed |
0 |
1 |
||
standard RNA-seq analysis pipeline (cloned from snakemake example workflow) |
last update 2020-11-03formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-02-15formatting: passedlinting: passed |
0 |
1 |
||
Adaption from https://github.com/snakemake-workflows/rna-seq-star-deseq2 for sRNA |
last update 2019-04-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-04-22formatting: failedlinting: failed |
0 |
1 |
||
Creating a synthetic tumor/normal sample pair from CHM1/CHM13 haploid cell lines. |
last update 2020-01-29formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2021-02-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-03-29formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2021-01-14formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-10-22formatting: failedlinting: failed |
0 |
1 |
||
A snakemake workflow for GATK following best practice guidelines |
last update 2019-08-26formatting: failedlinting: failed |
0 |
1 |
||
snakemake repository for alevin quantification of single cell RNAseq data |
last update 2020-06-17formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2019-10-21formatting: failedlinting: failed |
0 |
1 |
||
parse vcf |
last update 2021-01-18formatting: failedlinting: failed |
0 |
1 |
||
Conifer short-read polishing workflow |
workflow snakemake bioinformatics |
last update 2020-06-17formatting: failedlinting: failed |
0 |
1 |
|
Using https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling as the template |
last update 2020-04-28formatting: failedlinting: failed |
0 |
0 |
||
Using snakemake-workflows/dna-seq-gatk-variant-calling as a template |
last update 2020-02-27formatting: failedlinting: failed |
0 |
1 |
||
阪大用 |
last update 2019-10-25formatting: failedlinting: failed |
0 |
1 |
||
RNAseq workflow using snakemake workflow with Kallisto. |
last update 2020-09-10formatting: failedlinting: failed |
0 |
1 |
||
bwa map fastq files |
last update 2020-05-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-10-02formatting: failedlinting: failed |
0 |
1 |
||
snakemake gatk best practices 20200522 |
last update 2020-05-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-02-28formatting: failedlinting: failed |
0 |
1 |
||
🚰 Snakemake files for dahak workflows. Snakemake files for dahak workflows. (This repo will be absor… |
last update 2018-03-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-12-06formatting: failedlinting: failed |
0 |
1 |
||
template SNP calling |
last update 2019-07-29formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2019-09-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-03-20formatting: failedlinting: failed |
0 |
1 |
||
WGS pipeline using Snakemake |
last update 2020-01-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-05-13formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for generating native space hcp-mmp segmentations (requires Freesurfer run) |
last update 2021-01-22formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-01-27formatting: failedlinting: failed |
0 |
1 |
||
AW |
last update 2018-06-08formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2019-09-14formatting: failedlinting: failed |
0 |
1 |
||
Using the snakemake-workflow as a template to create my own WES pipeline |
last update 2019-07-04formatting: failedlinting: failed |
0 |
0 |
||
snakemake pipeline for calling uk biobank exomes |
last update 2020-06-11formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2020-06-10formatting: failedlinting: failed |
0 |
1 |
||
A pipeline for processing 16S / ITS data |
last update 2021-03-09formatting: failedlinting: failed |
0 |
1 |
||
Conifer long-read polishing workflow |
workflow snakemake bioinformatics |
last update 2020-06-17formatting: failedlinting: failed |
0 |
1 |
|
Clone of the Snakemake workflow for variant calling with the GATK pipeline |
last update 2020-01-23formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2020-12-07formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2019-08-03formatting: failedlinting: failed |
0 |
0 |
||
test |
last update 2020-03-27formatting: failedlinting: failed |
0 |
1 |
||
This Snakemake pipeline implements the GATK best-practices workflow for calling short germline varia… |
last update 2020-11-20formatting: failedlinting: failed |
0 |
1 |
||
Long read alignment pipelines |
last update 2021-03-09formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2021-03-10formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2019-11-12formatting: failedlinting: failed |
0 |
1 |
||
Assembling short genomic reads from bacteria |
last update 2019-09-26formatting: failedlinting: failed |
0 |
1 |
||
Small snakemake pipeline to explore RNA-Seq data with deepTools. |
snakemake-pipeline rna-seq |
last update 2020-07-03formatting: failedlinting: failed |
0 |
1 |
|
template of single cell sequencing from scilife |
last update 2020-06-29formatting: failedlinting: failed |
0 |
1 |
||
Analysis of publicly available MCF10A ChIP-Seq data |
last update 2021-01-29formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2018-08-02formatting: failedlinting: failed |
0 |
1 |
||
Rebasing changes made by @lucren on newest stag-mwc branch |
last update 2021-04-13formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-01-12formatting: failedlinting: failed |
0 |
1 |
||
Snakemake workflow for CircRNA Detection and Quantification |
last update 2019-05-20formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2021-01-12formatting: failedlinting: failed |
0 |
1 |
||
minimal snakemake repo for mixing R and python scripts |
last update 2019-12-18formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2019-09-17formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2019-10-04formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-01-21formatting: passedlinting: passed |
0 |
1 |
||
No description available. |
last update 2020-08-14formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline to automate a standard PSASS workflow |
last update 2021-03-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2019-10-22formatting: failedlinting: failed |
0 |
2 |
||
A Snakemake Workflow for Gene Set Enrichment Analysis |
last update 2020-04-16formatting: failedlinting: failed |
0 |
1 |
||
Process raw Quant-Seq data and run DE-Seq |
last update 2020-08-12formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2018-06-08formatting: failedlinting: failed |
0 |
0 |
||
Basic Snakemake wf for wordcloud generation. |
last update 2021-02-11formatting: failedlinting: failed |
0 |
1 |
||
The ENCODE-DCC demo workflow in Snakemake (under development) |
encode-dcc snakemake snakemake-workflows |
last update 2019-09-01formatting: failedlinting: failed |
0 |
1 |
|
no more boiler plate in your execution scripts. |
last update 2020-07-30formatting: failedlinting: failed |
0 |
3 |
||
Workflow to generate gene expression box plot for tissues |
last update 2019-11-20formatting: failedlinting: failed |
0 |
2 |
||
This is a pipeline for the beginning analysis of paired end ATAC seq data |
last update 2021-02-11formatting: failedlinting: failed |
0 |
3 |
||
No description available. |
last update 2021-04-27formatting: failedlinting: failed |
0 |
2 |
||
Snakemake pipeline for generation of GISTIC focal alteration frequencies from sWGS absolute copy num… |
last update 2020-10-09formatting: failedlinting: failed |
0 |
1 |
||
A workflow for getting gene information based on RNA-Seq data |
last update 2018-06-07formatting: failedlinting: failed |
0 |
0 |
||
Snakemake, OpenMS, and more |
last update 2017-12-14formatting: failedlinting: failed |
0 |
1 |
||
Snakemake pipeline for quality control using Fastqc and Fastq Screen |
last update 2019-09-26formatting: failedlinting: passed |
0 |
1 |
||
Evaluation workflow for Bitpacked Hopscotch Hashtable. |
last update 2021-01-05formatting: failedlinting: failed |
0 |
1 |
||
A benchmark of benchmark workflow |
last update 2019-11-27formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-02-03formatting: failedlinting: failed |
0 |
1 |
||
Evaluation Workflow for Protein Complex Similarity based on Weisfeiler-Lehman labeling |
last update 2021-01-27formatting: failedlinting: failed |
0 |
2 |
||
Workflow for generating reference phylogenies of AMR sequences in CARD |
last update 2020-07-30formatting: failedlinting: failed |
0 |
1 |
||
Collection of scripts for conveniently downloading data from the archs4 resource |
last update 2019-02-09formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2019-12-10formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2019-06-14formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2020-06-26formatting: failedlinting: failed |
0 |
1 |
||
Snakemake Pipeline for RNASeq Workflow |
last update 2018-12-10formatting: failedlinting: failed |
0 |
0 |
||
project for pp4rs 2020 |
last update 2020-03-12formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2020-09-09formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2021-03-26formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2019-08-02formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2016-12-07formatting: failedlinting: failed |
0 |
1 |
||
SV calling pipeline |
last update 2021-04-25formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2018-12-06formatting: failedlinting: failed |
0 |
1 |
||
Simple text analysis using Snakemake |
last update 2019-10-29formatting: failedlinting: failed |
0 |
1 |
||
A workflow for metagenomics analysis |
last update 2015-03-25formatting: failedlinting: failed |
0 |
0 |
||
No description available. |
last update 2021-03-23formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2020-12-18formatting: failedlinting: passed |
0 |
1 |
||
No description available. |
last update 2015-05-30formatting: failedlinting: failed |
0 |
2 |
||
No description available. |
last update 2021-04-09formatting: failedlinting: failed |
0 |
3 |
||
Alignment based workflow for Illumina Short reads |
last update 2020-07-29formatting: failedlinting: failed |
0 |
2 |
||
Estimate pi using a snakemake workflow |
last update 2020-12-17formatting: failedlinting: failed |
0 |
1 |
||
Snakemake Workflow: Impute HLA and/or KIR alleles from SNPs |
last update 2020-05-16formatting: failedlinting: failed |
0 |
1 |
||
Code to run the analysis of the Ultra Deep Sequencing |
last update 2017-10-19formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2019-05-20formatting: failedlinting: failed |
0 |
1 |
||
No description available. |
last update 2020-02-09formatting: failedlinting: failed |
0 |
2 |
||
My personal snakemake pipeline for VAST-TOOLS execution |
snakemake-pipeline rna-seq alternative-splicing |
last update 2020-09-04formatting: failedlinting: failed |
0 |
1 |
|
The assignment for the course PP4RS 2019 |
last update 2019-03-11formatting: failedlinting: failed |
0 |
0 |
||
build xaringan slides with snakemake |
xaringan xaringan-slides snakemake snakemake-workflow |
last update 2021-03-14formatting: failedlinting: failed |
0 |
1 |
|
A Snakemake workflow for analyzing AMBER molecular dynamics simulations. |
snakemake-workflow molecular-dynamics reproducible-research amber |
last update 2021-03-21formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2020-08-04formatting: failedlinting: failed |
0 |
0 |
||
Repository to process ITS amplicon sequencing data and produce figures for Schneider et al (2021) |
amplicon-data-preprocessing snakemake-workflow |
last update 2021-03-01formatting: failedlinting: failed |
0 |
0 |
|
old repo. see dib-lab/elvers for this snakemake workflow |
last update 2019-04-09formatting: failedlinting: failed |
0 |
1 |
||
Houses a snakemake workflow used for multiple sequence alignment and maximum likelihood phylogeny co… |
phylogenetic-trees alignment snakemake-workflows |
last update 2020-12-14formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
workflow ngs rna |
last update 2020-09-24formatting: failedlinting: failed |
0 |
8 |
|
Detect replication slippage variants at microsatellite regions |
bioinformatics-pipeline snakemake-workflows reproducible-workflows microsatellite-instability |
last update 2020-04-10formatting: failedlinting: failed |
0 |
1 |
|
No description available. |
last update 2020-08-06formatting: failedlinting: passed |
0 |
1 |
||
Snakemake tutorial ready to be used |
last update 2017-07-22formatting: failedlinting: failed |
0 |
0 |
||
An introduction to Snakemake with simple examples of central snakemake features |
last update 2020-11-06formatting: failedlinting: failed |
0 |
1 |
||
Scripts associated with our study, Genomic and transcriptomic characterization of relapsed small cel… |
last update 2021-02-26formatting: failedlinting: failed |
0 |
3 |