Pinned Repositories
chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).
cookiecutter-snakemake-workflow
A cookiecutter template for Snakemake workflows
dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
dna-seq-varlociraptor
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
docs
Documentation of the Snakemake-Workflows project
ngs-test-data
A workflow for creating small NGS test data sets, useful for continuous integration.
rna-seq-kallisto-sleuth
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
single-cell-rna-seq
A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
snakemake-workflow-template
A template for standard compliant snakemake-workflows
Snakemake-Workflows's Repositories
snakemake-workflows/rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
snakemake-workflows/dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
snakemake-workflows/docs
Documentation of the Snakemake-Workflows project
snakemake-workflows/single-cell-rna-seq
A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
snakemake-workflows/dna-seq-varlociraptor
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
snakemake-workflows/snakemake-workflow-template
A template for standard compliant snakemake-workflows
snakemake-workflows/rna-seq-kallisto-sleuth
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
snakemake-workflows/cookiecutter-snakemake-workflow
A cookiecutter template for Snakemake workflows
snakemake-workflows/chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).
snakemake-workflows/ngs-test-data
A workflow for creating small NGS test data sets, useful for continuous integration.
snakemake-workflows/dna-seq-neoantigen-prediction
Snakemake workflow for neoantigen prediction
snakemake-workflows/single-cell-drop-seq
A SingleCell RNASeq pre-processing pipeline built on snakemake
snakemake-workflows/dna-seq-benchmark
A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets
snakemake-workflows/accel-amplicon-trimming
Snakemake workflow implementing Accel Amplicon (Swift) trimming guidelines.
snakemake-workflows/dna-seq-mtb
A flavor of https://github.com/snakemake-workflows/dna-seq-varlociraptor preconfigured for molecular tumor boards
snakemake-workflows/cyrcular-calling
A Snakemake workflow for ecDNA detection in Nanopore or Illumina sequencing reads derived from DNA samples enriched for circular DNA.
snakemake-workflows/cite-seq-alevin-fry-seurat
Snakemake workflow for CITE-seq analaysis with alevin-fry and seurat
snakemake-workflows/species-quantification
snakemake-workflows/rad-seq-stacks
snakemake-workflows/structure-based-screening
Workflow for screening massive amounts of small molecules (ligands) against a target (PDB-File)
snakemake-workflows/transcriptome-differential-expression
long read differential expression analysis
snakemake-workflows/dna-seq-short-read-circle-map
A snakemake workflow for calling extrachromosomal circular DNA in Illumina short-read sequencing data with Circle-Map