differential-expression-analysis

A Snakemake workflow and MrBiomics module for performing and visualizing differential analyses of NGS data powered by the R package limma.

A Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.

Differential Expression Analysis tool box R lang package for omics data

An R package to plot interactive three-way differential expression analysis

R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single-cell CRISPR screening data.

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

Multi-omics module that includes RNAseq, Epigenetics, and integrated multi-omics analyses developed as part of the NIGMS Sandbox project

Approaches to identify Differential Rhythmicity

A comprehensive quality-control and quantification RNA-seq pipeline

Software for intuitively doing Differential Gene Expression (DGE) analysis on Windows and GNU\Linux, based on R packages.

An awesome Oxford Nanopore Pipeline for direct RNA-sequencing

Material used for a course on transcriptomics, covering transcriptome assembly, transcriptome functional annotation, differential expression analysis, and functional annotation data mining

Consensus pathway analysis module developed by the University of Nevada at Reno

A library for differential expression and gene set enrichment analysis based on hydra and pydantic.

An R/Bioconductor package for DamID differential binding, gene transcription and chromatin accessibility analysis.

A Python package for mechanism-aware single-cell differential analysis. It partitions DE genes into transcription-driven versus stabilization-driven classes using nascent (unspliced) RNA residuals. Also supports conventional DE, functional enrichment (ORA, GSEA, GO, KEGG), and visualization.

crispyx is a Python package for scalable CRISPR and Perturb-seq screen analysis on disk-backed AnnData files. It provides streaming quality control, normalization, pseudobulk aggregation, and differential expression without loading the full count matrix into memory.

RNA-Seq Data Analysis in R: From Raw Counts to Differential Expression Analysis

gene ID conversion; Prepare Differential Expression Results for ORA and GSEA

GWAS of Postmortem Brain Samples Sheds Light on the Development of Schizophrenia and Bipolar Disorder