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

Transcript quantification import for modular pipelines

Compare different differential abundance and expression methods

Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches

R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/

Explore and download data from the recount3 project

This RNAseq data analysis tutorial is created for educational purpose

Differential expression and allelic analysis, nonparametric statistics

Sashimi plots for RNA-seq data using detected transcripts

Modeling and correcting fragment sequence bias for RNA-seq

DESeq2 or edgeR

Perform differential transcript usage (DTU) analysis of bulk or single-cell RNA-seq data. See documentation at:

Workflow for Sequenza, cellularity and ploidy

Analysing Capture Seq Count Data

R package for tissue-specific gene enrichment

RNAseq pipeline for alternative splicing junctions

My R scripts, primarily R plotting scripts + some genomics software including 16S rRNA metataxnomics and RNAseq

Code for the Recount project

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

Generate HTML report for a set of genomic regions or DESeq2/edgeR results