Top workflows by topic

  • topics were clustered by similarity using a language model

  • topics can be added by users by opening a pull request with updates to topics.json

  • only standardized workflows are included

  • follow the links to the individual workflow pages to get more information

Sequencing and Analysis (30)

Keywords

rna-seq genomics ngs sequencing rnaseq fastq bam vcf wgs wes long-reads long-read-sequencing nanopore nanopore-sequencing illumina pacbio pacbio-sequencing

Matching workflows

MPUSP/snakemake-simple-mapping massiddamt/rna_vc_docker WestGermanGenomeCenter/circrna_detection jma1991/rnaseq tucca-cellag/tucca-rna-seq solida-core/dima juliawiggeshoff/AugusMake lacklab/MuSTARRd FeelLiao/rna-seq-std sandragodinhosilva/melange MPUSP/snakemake-ont-basecalling MPUSP/snakemake-ont-bacterial-variants CVUA-RRW/FooDMe friendsofstrandseq/ashleys-qc-pipeline GooglingTheCancerGenome/sv-gen epigen/rnaseq_pipeline epigen/fetch_ngs epigen/spilterlize_integrate friendsofstrandseq/mosaicatcher-pipeline ncherric/Iliad epigen/genome_tracks sneuensc/mapache akcorut/kGWASflow epigen/dea_limma zavolanlab/zarp epigen/enrichment_analysis epigen/atacseq_pipeline snakemake-workflows/rna-seq-kallisto-sleuth GooglingTheCancerGenome/sv-callers cbg-ethz/V-pipe

Specific Sequencing Techniques (24)

Keywords

chip-seq atac-seq rna-seq-pipeline rnaseq-pipeline sciworkflows scrna-seq single-cell 10xgenomics cellranger seurat snrna-seq sn-rna-seq sc-rna-seq scrbseq scrb-seq dropseq drop-seq

Matching workflows

tdayris/fair_rnaseq_salmon_quant manuelphilip/Single-cell-analysis-Snakemake-workflow WestGermanGenomeCenter/circrna_detection tucca-cellag/tucca-rna-seq IMS-Bio2Core-Facility/polya_liftover IMS-Bio2Core-Facility/single_snake_sequencing nikostr/dna-seq-deepvariant-glnexus-variant-calling niekwit/rna-seq-star-tetranscripts nodrogluap/tamor epigen/rnaseq_pipeline DavideBrex/SpikeFlow epigen/spilterlize_integrate epigen/mixscape_seurat epigen/scrnaseq_processing_seurat epigen/dea_seurat epigen/genome_tracks akcorut/kGWASflow epigen/dea_limma epigen/enrichment_analysis epigen/atacseq_pipeline snakemake-workflows/rna-seq-kallisto-sleuth snakemake-workflows/dna-seq-varlociraptor snakemake-workflows/dna-seq-gatk-variant-calling snakemake-workflows/rna-seq-star-deseq2

Genomics and Genetics (24)

Keywords

genomics genomics-analysis genome-assembly genome-annotation genome genetics population-genetics population-genomics gwas variant-calling variant-effect-prediction genomic-variant-calling genomic-surveillance genomic-data-analysis genomic-prediction genomic-regions genomic-binning functional-annotation taxonomic-classifications

Matching workflows

milesroberts-123/slim-sweep-cnn MPUSP/snakemake-simple-mapping dbespiatykh/TBvar tdayris/fair_gatk_mutect2 ClavelLab/genome-assembly solida-core/dima nikostr/dna-seq-deepvariant-glnexus-variant-calling sandragodinhosilva/melange MPUSP/snakemake-ont-bacterial-variants friendsofstrandseq/ashleys-qc-pipeline epigen/fetch_ngs zjnolen/PopGLen LiaOb21/colora IKIM-Essen/uncovar friendsofstrandseq/mosaicatcher-pipeline ncherric/Iliad epigen/genome_tracks sneuensc/mapache akcorut/kGWASflow epigen/enrichment_analysis snakemake-workflows/dna-seq-varlociraptor moiexpositoalonsolab/grenepipe cbg-ethz/V-pipe snakemake-workflows/dna-seq-gatk-variant-calling

Data Science and Machine Learning (18)

Keywords

python r machine-learning deep-learning statistics data-science biomedical-data-science data-reduction data-visualization visualization dimensionality-reduction classification regression logistic-regression neural-network cnn-model cnn-keras random-forest xgboost deepvariant genomic-variant-calling genomic-prediction genomic-surveillance genomic-data-analysis genomic-binning functional-annotation taxonomic-classifications

Matching workflows

milesroberts-123/slim-sweep-cnn IMS-Bio2Core-Facility/polya_liftover nikostr/dna-seq-deepvariant-glnexus-variant-calling Crollo95/survhive-workflow epigen/rnaseq_pipeline SchlossLab/mikropml-snakemake-workflow epigen/spilterlize_integrate epigen/mixscape_seurat epigen/scrnaseq_processing_seurat epigen/dea_seurat epigen/genome_tracks epigen/dea_limma epigen/unsupervised_analysis epigen/enrichment_analysis epigen/atacseq_pipeline snakemake-workflows/dna-seq-varlociraptor moiexpositoalonsolab/grenepipe snakemake-workflows/dna-seq-gatk-variant-calling

Reproducibility and Workflow Management (18)

Keywords

reproducibility reproducible-research reproducible-science reproducible-workflows reproducible-paper workflow-automation workflow-management workflow-engine pipeline-framework analysis-workflows workflow-reusable workflows pipelines snakefile cwl github github-actions continuous-integration scientific-papers scientific-workflows apptainer singularity docker

Matching workflows

tdayris/fair_rnaseq_salmon_quant tdayris/fair_fastqc_multiqc tucca-cellag/tucca-rna-seq tdayris/fair_gatk_mutect2 solida-core/dima juliawiggeshoff/AugusMake TLenfers/multispecies_mitochondrial_variant_analysis IMS-Bio2Core-Facility/polya_liftover IMS-Bio2Core-Facility/GTExSnake IMS-Bio2Core-Facility/single_snake_sequencing nikostr/dna-seq-deepvariant-glnexus-variant-calling MPUSP/snakemake-bacterial-riboseq MPUSP/snakemake-ont-bacterial-variants zavolanlab/zarp snakemake-workflows/rna-seq-kallisto-sleuth snakemake-workflows/dna-seq-varlociraptor snakemake-workflows/dna-seq-gatk-variant-calling snakemake-workflows/rna-seq-star-deseq2

RNA Sequencing and Transcriptomics (17)

Keywords

rna-seq transcriptomics rna-seq-analysis rna-seq-pipeline rnaseq-pipeline rna-seq-snakemake rna-seq-data transcriptome transcriptome-assembly transcriptome-annotation differential-expression differential-expression-analysis differential-gene-expression bulk-rna-seq single-cell-rna-seq single-cell-rna-sequencing sc-rna-seq scrbseq scrb-seq dropseq drop-seq

Matching workflows

tdayris/fair_rnaseq_salmon_quant manuelphilip/Single-cell-analysis-Snakemake-workflow WestGermanGenomeCenter/circrna_detection tucca-cellag/tucca-rna-seq juliawiggeshoff/AugusMake IMS-Bio2Core-Facility/polya_liftover FeelLiao/rna-seq-std niekwit/rna-seq-star-tetranscripts boulardlab/3t-seq epigen/rnaseq_pipeline epigen/spilterlize_integrate epigen/dea_seurat epigen/genome_tracks epigen/dea_limma zavolanlab/zarp epigen/enrichment_analysis snakemake-workflows/rna-seq-kallisto-sleuth

Single-Cell Sequencing and Omics (16)

Keywords

single-cell scrna-seq sciworkflows 10xgenomics cellranger seurat snrna-seq sn-rna-seq sc-rna-seq scrbseq scrb-seq dropseq drop-seq spatial-omics spatialdata multiplexed-imaging

Matching workflows

manuelphilip/Single-cell-analysis-Snakemake-workflow tucca-cellag/tucca-rna-seq IMS-Bio2Core-Facility/polya_liftover IMS-Bio2Core-Facility/single_snake_sequencing nikostr/dna-seq-deepvariant-glnexus-variant-calling nodrogluap/tamor epigen/mixscape_seurat epigen/scrnaseq_processing_seurat epigen/dea_seurat epigen/genome_tracks akcorut/kGWASflow epigen/dea_limma snakemake-workflows/rna-seq-kallisto-sleuth snakemake-workflows/dna-seq-varlociraptor snakemake-workflows/dna-seq-gatk-variant-calling snakemake-workflows/rna-seq-star-deseq2

Cancer Genomics and Variants (15)

Keywords

cancer-genomics somatic-variants somatic-mutations taxonomic-classifications neoantigens neoantigen tumor-antigen neoepitopes neoepitope exitron indels mutations mutational-signatures hidden-markov-models genotype-likelihoods variant-annotations variant-annotation variant-functional-annotation variant-effect-prediction variant-calling genomic-variant-calling genomic-prediction genomic-surveillance genomic-data-analysis genomic-binning genomic-regions functional-annotation

Matching workflows

MPUSP/snakemake-simple-mapping dbespiatykh/TBvar tdayris/fair_gatk_mutect2 nikostr/dna-seq-deepvariant-glnexus-variant-calling MPUSP/snakemake-ont-bacterial-variants GooglingTheCancerGenome/sv-gen nodrogluap/tamor zjnolen/PopGLen IKIM-Essen/uncovar epigen/genome_tracks epigen/enrichment_analysis GooglingTheCancerGenome/sv-callers snakemake-workflows/dna-seq-varlociraptor moiexpositoalonsolab/grenepipe snakemake-workflows/dna-seq-gatk-variant-calling

Epigenomics and Methylation (10)

Keywords

methylation chip-seq atac-seq chip-seq-pipelines rrbs-pipeline rrbs-data-analysis bsseq emseq bisulfite bs-seq high-throughput-sequencing ibd-segments estimate-relationships low-coverage-sequencing dna-methylation bisulfite-sequencing em-seq strand-seq

Matching workflows

friendsofstrandseq/ashleys-qc-pipeline semenko/serpent-methylation-pipeline Zilong-Li/lcWGS-imputation-workflow DavideBrex/SpikeFlow epigen/spilterlize_integrate friendsofstrandseq/mosaicatcher-pipeline epigen/genome_tracks epigen/dea_limma epigen/enrichment_analysis epigen/atacseq_pipeline

Population Genetics and Genomics (7)

Keywords

population-genetics population-genomics gwas ancestry admixture ancient-dna ancientdna kinship population-structure population-density-maps population-evolution genetic-linkage-analysis genetic-linkage linkage genetic-mapping mapping genetic-association association-study genome-wide-association-study genome-wide-association association-mapping gwas-pipeline gwas-tools limma limma-trend limma-voom

Matching workflows

milesroberts-123/slim-sweep-cnn MPUSP/snakemake-simple-mapping zjnolen/PopGLen sneuensc/mapache akcorut/kGWASflow epigen/dea_limma moiexpositoalonsolab/grenepipe

Evolution and Phylogenetics (5)

Keywords

evolution phylogenetics comparative-genomics population-genetics population-genomics gwas phylogenomics phylogeny phylogenetic-placement phylogenetic-compression phylogenetic-diversity molecular-evolution gene-families protein-families orthology orthology-inference orthoevol homology

Matching workflows

milesroberts-123/slim-sweep-cnn tahiri-lab/aPhyloGeo-pipeline zjnolen/PopGLen akcorut/kGWASflow moiexpositoalonsolab/grenepipe

Metagenomics and Microbiome (3)

Keywords

metagenomics microbiome metagenomic-analysis metagenomic-pipeline metagenomic-classification metatranscriptomics metatranscriptomic-pipeline microbial-genomics microbiome-analysis microbial-ecology metabolic-models gut-microbiome mags flux-balance-analysis genome-scale-metabolic-model metabolic-modeling

Matching workflows

emmaewade/pangenome-workflow fischuu/Pipeline-Holoruminant-Meta franciscozorrilla/metaGEM

Genome Assembly and Scaffolding (3)

Keywords

genome-assembly assembly scaffolding genome-scaffolding organelle-assembler chromosome-level-assembly karyotype genome-browser genome-track

Matching workflows

ClavelLab/genome-assembly LiaOb21/colora epigen/genome_tracks

Energy Systems and Modeling (0)

Keywords

energy renewable-energy power-systems power-system power-system-planning energy-systems energy-system energy-system-modeling energy-system-model energy-system-planning energy-transition modelling optimization sector-coupling demand-flexibility dynamic-bayesian-network

Matching workflows