Snakemake-Workflows (@snakemake-workflows)
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snakemake-workflows

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  • Stars
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    1,194
  • Global Org. Rank 13,639 (Top 5 %)
  • Registered over 7 years ago
  • Most used languages
    Python
         88.9 %
    R
         11.1 %

Top repositories

1

rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2
Python
318
star
2

dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow
Python
238
star
3

docs

Documentation of the Snakemake-Workflows project
151
star
4

single-cell-rna-seq

A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
R
97
star
5

snakemake-workflow-template

A template for standard compliant snakemake-workflows
Python
85
star
6

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
82
star
7

rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
Python
64
star
8

cookiecutter-snakemake-workflow

A cookiecutter template for Snakemake workflows
Python
56
star
9

chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).
Python
26
star
10

ngs-test-data

A workflow for creating small NGS test data sets, useful for continuous integration.
Python
21
star
11

dna-seq-neoantigen-prediction

Snakemake workflow for neoantigen prediction
Python
14
star
12

dna-seq-benchmark

A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets
Python
11
star
13

dna-seq-mtb

A flavor of https://github.com/snakemake-workflows/dna-seq-varlociraptor preconfigured for molecular tumor boards
Python
4
star
14

cyrcular-calling

A Snakemake workflow for ecDNA detection in Nanopore or Illumina sequencing reads derived from DNA samples enriched for circular DNA.
Python
3
star
15

species-quantification

Python
2
star
16

cite-seq-alevin-fry-seurat

Snakemake workflow for CITE-seq analaysis with alevin-fry and seurat
R
2
star
17

transcriptome-differential-expression

long read differential expression analysis
Python
1
star
18

rad-seq-stacks

Python
1
star
19

structure-based-screening

Workflow for screening massive amounts of small molecules (ligands) against a target (PDB-File)
Python
1
star