RNAseq analysis notes from Ming Tang

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

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

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

A single-cell RNAseq pipeline for 10X genomics data

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data