Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads

Interactive R package to quantify, analyse and visualise alternative splicing

Workshop • Analysis of RNA-seq data

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

ASAP : Automated Single-cell Analysis Pipeline

Gene-level general linear mixed model

Script to automate differential expression analysis using DESeq2, edgeR or limma-voom

📊 An R package of RNA-seq workflow

single cell and bulk RNASeq analysis scripts

An application for exploring and visualizing differential gene expression data created with DESeq2

Code and figures for the Differential Causal Inference (DCI) algorithm

Curare - A customizable and reproducible analysis pipeline for RNA-Seq experiments

Scripts to run differential expression analysis using DESeq2 package

🍊 View the gene expression response to TNF and IL-17A with vanilla Javascript and HTML.

Comparison of gene usage in immune repertoires under different biological conditions

Viper is a Snakemake workflow, aimed at performing the RNA-seq workflow of the paper 'Causes and consequences of a glutamine induced normoxic HIF1 activity for the tumor metabolism', Kappler et al. (2019) in a reproducible and automated manner

Python framework for explainable omics analysis

RNA-seq alignment and analysis pipeline

Temporal Integrative Genomics Analysis in R

These are tutorials on a subset of tools available for processing raw RNAseq data. This if for HISAT2_SAMtools_Stringtie_gffcompare_ballgown pipeline or HISAT2_SAMtools_Stringtie_PrepDEanalysis.py_DESeq2 pipeline