ArticleNucleic acids research2025
edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 528 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
528 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- TranDep: a transcriptomics atlas of depression.Molecular psychiatry · 2026Article
- Response to geographic song variation predicts differential gene expression in the blood of a songbird.iScience · 2026Article
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- Sexual dimorphism in epidermal stem cell dynamics.Nature · 2026Article
- Genetic variation in a plant-parasitic nematode is associated with host gene expression changes conserved across evolutionarily distant host plants.G3 (Bethesda, Md.) · 2026Article
- Developmental divergence in gene regulation underlies trophic innovation in Lake Victoria cichlids.Proceedings. Biological sciences · 2026Article
- CXCR4+ circulating tumor cells (CTCs) accumulate in subcutaneous, immune suppressive, CXCL12-loaded-hydrogel.Materials today. Bio · 2026Article
- CD137 agonists in mice suppress germinal center responses by increasing the immunosuppressive activity of follicular regulatory T-cells.The EMBO journal · 2026Article
- Active transcriptome remodeling underlies antimony-induced drug tolerance in persister-like Leishmania parasites.PLoS pathogens · 2026Article
- Article
- KDM6A loss enhances oxidative phosphorylation uncovering tissue-level convergent evolution.The EMBO journal · 2026Article
- Mechanosignaling promotes macrophage apoptosis resistance in pulmonary fibrosisbioRxiv : the preprint server for biology · 2026Article
- Functional-Taxonomic Scaling Resolves Conflicting Average Genome Size Estimates Across Environmental Gradients.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- FedEdgeR: federated and privacy-preserving edgeR for differential gene expression analysis.bioRxiv : the preprint server for biology · 2026Article
468 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
edgeR is an R/Bioconductor software package for differential analyses of sequencing data in the form of read counts for genes or genomic features. Over the past 15 years, edgeR has been a popular choice for statistical analysis of data from sequencing technologies such as RNA-seq or ChIP-seq. edgeR pioneered the use of the negative binomial distribution to model read count data with replicates and the use of generalized linear models to analyze complex experimental designs. edgeR implements empirical Bayes moderation methods to allow reliable inference when the number of replicates is small. This article announces edgeR version 4, which includes new developments across a range of application areas. Infrastructure improvements include support for fractional counts, implementation of model fitting in C and a new statistical treatment of the quasi-likelihood pipeline that improves accuracy for small counts. The revised package has new functionality for differential methylation analysis, differential transcript expression, differential transcript and exon usage, testing relative to a fold-change threshold and pathway analysis. This article reviews the statistical framework and computational implementation of edgeR, briefly summarizing all the existing features and functionalities but with special attention to new features and those that have not been described previously.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.