edgeR is a tool for differential expression (DE) analysis of RNA-seq, ChIP-seq, CAGE, and SAGE data with biological replicates. The edgeR algorithm uses information from all the genes, computes the dispersion using a weighted likelihood and F-test techniques. For the normalization, it can use the trimmed mean of M-values, upper-quartile (UQ) procedure, Relative Log Expression (RLE), and DESeq. It can compare two groups, paired and unpaired, or use a Generalized Linear Model (GLM). The upper-quartile (UQ) procedure is also applicable to single-cell RNA-seq (scRNA-seq).
RNA-Seq; ChIP-seq
McCarthy DJ, Chen Y, Smyth GK "Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation." Nucleic Acids Res. 2012 May;40(10):4288-97. Jan 28. https://doi.org/10.1093/nar/gks042
PMID: 22287627
PMCID: PMC3378882
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600
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