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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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