edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets

Chen, Y; Chen, L; Lun, ATL; Baldoni, PL; Smyth, GK

Author(s): Chen, Y; Chen, L; Lun, ATL; Baldoni, PL; Smyth, GK;
Details: Publication Year 2025-01-11,Volume 53,Issue #2,Page gkaf018
Journal Title: Nucleic Acids Research
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.
Publisher: Oxford Academic
Keywords: *Software; Bayes Theorem; Humans; High-Throughput Nucleotide Sequencing/methods; Gene Expression Profiling/methods; DNA Methylation; Sequence Analysis, RNA/methods
Research Division(s): Bioinformatics and Computational Biology
PubMed ID: 39844453
Publisher's Version: https://doi.org/10.1093/nar/gkaf018
Open Access at Publisher's Site: https://doi.org/10.1093/nar/gkaf018.
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2025-02-07 02:57:12

Last Modified: 2025-02-07 03:13:23