Snakemake-Workflows

Repositories

• dna-seq-varlociraptor

  Variant detection with Delly and Freebayes, followed by statistical assessment with Varlociraptor
  HTML MIT 5 17 0 4 Updated Jun 18, 2020

• chipseq

  ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).
  Python MIT 0 4 0 0 Updated Jun 16, 2020

• dna-seq-gatk-variant-calling

  This Snakemake pipeline implements the GATK best-practices workflow

  snakemake reproducibility sciworkflows
  Python MIT 78 104 8 2 Updated Jun 1, 2020

• rna-seq-kallisto-sleuth

  A workflow for RNA-seq differential expression analysis based on Kallisto and Sleuth.
  R MIT 24 24 4 2 Updated Apr 28, 2020

• cookiecutter-snakemake-workflow

  A cookiecutter template for Snakemake workflows

  snakemake snakemake-workflows cookiecutter-template
  Python MIT 25 30 0 0 Updated Apr 15, 2020

• rna-seq-star-deseq2

  RNA-seq workflow using STAR and DESeq2

  rna-seq snakemake ngs reproducible-science snakemake-workflows
  Python MIT 100 135 5 3 Updated Mar 10, 2020

• single-cell-rna-seq

  A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
  R MIT 28 54 1 0 Updated Feb 14, 2020

• docs

  Documentation of the Snakemake-Workflows project

  snakemake snakemake-workflows
  MIT 12 77 3 0 Updated Jan 21, 2020

• ngs-test-data

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

  snakemake ngs snakemake-workflows
  Python 9 15 0 1 Updated Dec 11, 2019

• single-cell-drop-seq

  Forked from Hoohm/dropSeqPipe

  A SingleCell RNASeq pre-processing pipeline built on snakemake
  R CC-BY-SA-4.0 36 9 0 0 Updated Oct 29, 2019

• accel-amplicon-trimming

  Forked from clinical-genomics-uppsala/accel_amplicon_trimming

  Snakemake workflow implementing Accel Amplicon (Swift) trimming guidelines.
  Python MIT 2 4 0 0 Updated May 18, 2019