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

🧬 gget enables efficient querying of genomic reference databases

RNAseq analysis notes from Ming Tang

https://www.sc-best-practices.org

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

Tools to process and analyze deep sequencing data.

Near-optimal RNA-Seq quantification

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

NicheNet: predict active ligand-target links between interacting cells

A repository for setting up a RNAseq workflow

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

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

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

Table of software for the analysis of single-cell RNA-seq data.

Differential analysis of RNA-Seq

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

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

minimal example implementations for bioinformatics workflow managers

Fast and accurate gene fusion detection from RNA-Seq data