Snakemake-Workflows

rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2

Python 178 MIT 138 7 5
rna-seq-kallisto-sleuth
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

R 39 MIT 43 5 3
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.

Python 40 MIT 20 2 5
chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).

Python 12 MIT 10 0 1
dna-seq-neoantigen-prediction
Snakemake workflow for neoantigen prediction

Python 4 MIT 2 7 0
cite-seq-alevin-fry-seurat
Snakemake workflow for CITE-seq analaysis with alevin-fry and seurat

R 2 0 0 0
dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow

Python 144 MIT 105 8 2
snakemake-workflow-template
A cookiecutter template for a snakemake-workflow readme file

Python 3 1 0 0
cookiecutter-snakemake-workflow
A cookiecutter template for Snakemake workflows

Python 46 MIT 36 2 1
rad-seq-stacks

Python 0 MIT 1 8 0

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