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Snakemake-Workflows

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  1. docs docs Public

    Documentation of the Snakemake-Workflows project

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Repositories

Showing 10 of 26 repositories
  • rna-seq-kallisto-sleuth Public

    A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

    snakemake-workflows/rna-seq-kallisto-sleuth’s past year of commit activity
    Python 68 MIT 45 7 2 Updated Jul 22, 2025
  • dna-seq-varlociraptor Public

    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/dna-seq-varlociraptor’s past year of commit activity
    Python 86 MIT 42 8 14 Updated Jul 21, 2025
  • dna-seq-benchmark Public

    A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets

    snakemake-workflows/dna-seq-benchmark’s past year of commit activity
    Python 12 MIT 3 7 4 Updated Jul 15, 2025
  • cellranger-count Public

    A Snakemake workflow for counting single cell RNAseq (scRNA-seq) data with Cell Ranger (Cell Ranger licensing requires a manual download of the software).

    snakemake-workflows/cellranger-count’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jul 11, 2025
  • rna-longseq-de-isoform Public

    long read differential expression analysis and splice variant analysis

    snakemake-workflows/rna-longseq-de-isoform’s past year of commit activity
    Python 3 MIT 1 8 2 Updated Jul 4, 2025
  • snakemake-workflow-template Public template

    A template for standard compliant snakemake-workflows

    snakemake-workflows/snakemake-workflow-template’s past year of commit activity
    Python 105 MIT 38 1 1 Updated Jun 23, 2025
  • dna-seq-short-read-circle-map Public

    A snakemake workflow for calling extrachromosomal circular DNA in Illumina short-read sequencing data with Circle-Map

    snakemake-workflows/dna-seq-short-read-circle-map’s past year of commit activity
    Python 0 MIT 0 0 2 Updated Jun 16, 2025
  • effect-size-estimation Public

    Generic, uncertainty aware, parameter free effect size estimation

    snakemake-workflows/effect-size-estimation’s past year of commit activity
    Python 0 0 0 0 Updated May 15, 2025
  • dna-seq-mtb Public

    A flavor of https://github.com/snakemake-workflows/dna-seq-varlociraptor preconfigured for molecular tumor boards

    snakemake-workflows/dna-seq-mtb’s past year of commit activity
    Python 4 MIT 2 0 1 Updated Mar 26, 2025
  • oncology Public

    A work in progress Snakemake workflow for cohort studies in oncology

    snakemake-workflows/oncology’s past year of commit activity
    2 0 0 0 Updated Dec 10, 2024