snakemake-workflows/rna-seq-star-deseq2

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

Customizable workflows based on snakemake and python for the analysis of NGS data

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Gene Set Enrichment Analysis in Python

scRNAseq analysis notes from Ming Tang

Tools to process and analyze deep sequencing data.

This is the development home of the workflow management system Snakemake. For general information, see