DESeq2 or edgeR

A front-end GUI to map NGS DNA sequencing data using HISAT backend tool. This software offers robust seamless queueing of the mapping operations along with parameter memory for quick and easy customization.

Useful wrappers and functions for RNA-Seq analysis

PiReT web interface

RNA Seq Workflow

An R package to parse and manage text output of the sequencing quality control utility (fastQC)

An example RNA-seq pipeline with Nextflow and using public ENCODE data

Submission for the Bioinformatics Peer Prize 2018

A prior learning and sampling model informed tool for learning with Single Cell RNA-Seq data

Tutorial test

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Analysis of RNA-seq data using DESeq2

Differential expression analysis in R for RNA sequence reads of fission yeast.

Analysing Capture Seq Count Data

Enhanced volcano plot using edgeR data

Contribute your human Illumina RNA-seq data to recount2

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

An R interface to query and extract data from the ARCHS4 data