RNA-seq workflow using STAR and DESeq2

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

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

A complete workflow for analyzing and visualizing bulk RNA-seq data.

Perform differential analysis from FastQ files with Salmon, tximport, and DESeq2

Iteratively randomly pooling scRNA-seq expressing a given gene from different numbers of cells and running DESeq2 with fdrtools correction to determine how many times which genes come out as enriched with said gene

sg4_DExplore is an interactive bioinformatics platform designed for the seamless exploration and functional interpretation of RNA-Seq differential expression data. Developed specifically for researchers working with DESeq2 outputs, the tool automates the tedious steps of gene ID mapping, statistical filtering, and pathway enrichment.

Reproducible RNA-seq pipeline using Snakemake — QC, trimming, STAR alignment, featureCounts, DESeq2

End-to-end Snakemake pipeline for pan-cancer multi-omic analysis (QC, RNA-seq alignment, differential expression, variant calling, MSI/TMB scoring, and microbiome profiling)

Analysing RNA sequencing data with DESeq2.

This repository contains an example implementation of DESeq2 in Python.

Compilation of scripts pertaining to the field of Bioinformatics

Some useful scripts useful for parsing or writing DESeq2 Scripts

Workflow to simulate an RNA-seq reads and perform DE-analysis

Quantify peaks in BED format to a sparse count matrix for downstream analysis, such as DEseq2.