deseq2

RNA-seq workflow using STAR and DESeq2

Brings bulk and pseudobulk transcriptomics to the tidyverse

Transcript quantification import for modular pipelines

Statistical Analysis of RNA-Seq Tools

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

Volcano plots for differential expression in R. Reads DESeq2, edgeR and limma output directly; highlight genes of interest and compose gene tables with gt.

Feature-rich Python implementation of the tximport package for gene count estimation.

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

This RNAseq data analysis tutorial is created for educational purpose

NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization

Differential gene expression analysis and pathway analysis of RNAseq data

DESeq2 or edgeR

RNA-seq Analysis Pipeline Testing and Optimization Resource - Intelligent pipeline selection and comprehensive benchmarking.

TUCCA's RNA-Seq Workflow for Read Quantification, Differential Expression, and Pathway Enrichment Analysis

A quick recap of widely used differential analyses methods in R for RNA-seq experiments

Differential expression analysis: DESeq2, edgeR, limma. Realized in python based on rpy2

single cell and bulk RNASeq analysis scripts

a web-based R shiny application that wraps DESeq2 R package