Snakemake-Workflows (snakemake-workflows)

Snakemake-Workflows

snakemake-workflows

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Snakemake-Workflows's repositories

rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

Language:PythonLicense:MITStargazers:299Issues:12Issues:36

dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

Language:PythonLicense:MITStargazers:232Issues:9Issues:26

docs

Documentation of the Snakemake-Workflows project

single-cell-rna-seq

A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.

Language:RLicense:MITStargazers:92Issues:8Issues:4

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.

Language:PythonLicense:MITStargazers:81Issues:9Issues:12

snakemake-workflow-template

A template for standard compliant snakemake-workflows

Language:PythonLicense:MITStargazers:72Issues:2Issues:5

rna-seq-kallisto-sleuth

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

Language:PythonLicense:MITStargazers:63Issues:7Issues:17

cookiecutter-snakemake-workflow

A cookiecutter template for Snakemake workflows

Language:PythonLicense:MITStargazers:54Issues:4Issues:3

chipseq

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

Language:PythonLicense:MITStargazers:24Issues:3Issues:1

ngs-test-data

A workflow for creating small NGS test data sets, useful for continuous integration.

dna-seq-neoantigen-prediction

Snakemake workflow for neoantigen prediction

Language:PythonLicense:MITStargazers:13Issues:5Issues:8

single-cell-drop-seq

A SingleCell RNASeq pre-processing pipeline built on snakemake

Language:PythonLicense:CC-BY-SA-4.0Stargazers:12Issues:3Issues:0

dna-seq-benchmark

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

Language:PythonLicense:MITStargazers:10Issues:1Issues:0

accel-amplicon-trimming

Snakemake workflow implementing Accel Amplicon (Swift) trimming guidelines.

Language:PythonLicense:MITStargazers:4Issues:3Issues:0

cyrcular-calling

A Snakemake workflow for ecDNA detection in Nanopore or Illumina sequencing reads derived from DNA samples enriched for circular DNA.

Language:PythonLicense:MITStargazers:3Issues:2Issues:7

dna-seq-mtb

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

Language:PythonLicense:MITStargazers:3Issues:0Issues:0

cite-seq-alevin-fry-seurat

Snakemake workflow for CITE-seq analaysis with alevin-fry and seurat

Language:RStargazers:2Issues:0Issues:0
Language:PythonLicense:MITStargazers:2Issues:0Issues:0

structure-based-screening

Workflow for screening massive amounts of small molecules (ligands) against a target (PDB-File)

Language:PythonLicense:MITStargazers:1Issues:1Issues:0

dna-seq-short-read-circle-map

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

Language:PythonLicense:MITStargazers:0Issues:0Issues:0

transriptome-differential-expression

long read differential expression analysis

Language:PythonLicense:MPL-2.0Stargazers:0Issues:0Issues:0