edgeR swMATH ID: 6936 Software Authors: Mark D. Robinson; Davis J. McCarthy; Gordon K. Smyth Description: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. t is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data. Homepage: http://www.bioconductor.org/ Keywords: Bioinformatics Related Software: Bioconductor; R; DEseq; Voom; BaySeq; DESeq2; TopHat; KEGG; limma; gcrma; DEGseq; RSEM; EBSeq; ggplot2; CRAN; STAR; HTSeq; igraph; ShrinkBayes; Galaxy Cited in: 52 Documents all top 5 Cited by 187 Authors 4 Nettleton, Dan 3 Liu, Peng 3 Smyth, Gordon K. 3 Witten, Daniela M. 2 Dudoit, Sandrine 2 Gill, Ryan S. 2 Li, Hongzhe 2 Lun, Aaron T. L. 2 Robin, Stéphane 2 Robinson, Mark D. 2 Zhao, Hongyu 1 Ajdic, Dragana 1 Akalin, Altuna 1 Alexander, Warren S. 1 Aransay, Ana M. 1 Bacallado, Sergio 1 Bandara, Udika 1 Beißbarth, Tim 1 Bi, Ran 1 Bickel, Peter John 1 Boer, Judith M. 1 Boley, Nathan 1 Bonafede, Elisabetta 1 Brown, James Bentley 1 Celeux, Gilles 1 Chen, Mengjie 1 Chen, Na-Mi 1 Chen, Yunshun 1 Cheng, Ruihua 1 Christensen, Brock C. 1 Chung, Dongjun 1 Clarke, Bertrand S. 1 Clarke, Jennifer Lynn 1 Cleynen, Alice 1 Collado Torres, Leonardo 1 Crowell, Helena L. 1 Cui, Shiqi 1 Dadaneh, Siamak Zamani 1 Datta, Somnath 1 Datta, Susmita 1 Davis, Sean L. 1 de Menezes, Renée X. 1 Delgado, Alberto Santos 1 Dobra, Adrian 1 Du, Ruofei 1 Fandohan, Adandé Belarmain 1 Fang, Zhide 1 Favaro, Stefano 1 Feng, Dai 1 Ferreira, Marco A. R. 1 Franke, Verdan 1 Frazee, Alyssa C. 1 Gallopin, Mélina 1 Gharaibeh, Raad Z. 1 Ghosh, Debashis 1 Girirajan, Santhosh 1 Gonçalves, Flávio Bambirra 1 Guha, Subharup 1 Haas, Stefan A. 1 Hackenberg, Michael 1 Hansen, Kasper D. 1 Hoen, Anne G. 1 Holmes, Susan P. 1 Hou, Lin 1 Hu, Yijuan 1 Huang, Haiyan 1 Huang, Lijun 1 Huttenhower, Curtis 1 Ibrahim, Joseph George 1 Irizarry, Rafael A. 1 Jaffe, Andrew E. 1 Jaffrézic, Florence 1 Jeganathan, Pratheepa 1 Jeong, Seongmun 1 Ji, Tieming 1 Jiang, Hui 1 Jobin, Christian 1 Johnson, Marla 1 Jung, Klaus 1 Kakaï, Romain Glèlè 1 Kalscheuer, Vera 1 Karagas, Margaret R. 1 Keith, Jonathan M. 1 Keles, Sunduz 1 Kong, Yan 1 Kotoka, Ekua 1 Kramer, Frank 1 Kruppa, Jochen 1 Landau, Will 1 Langmead, Ben 1 Lee, Juhee 1 Lee, Stanley 1 Leek, Jeffrey T. 1 Li, Mingfeng 1 Li, Zhigang 1 Lim, David K. 1 Lin, Shili 1 Lin, Zhixiang 1 Lithio, Andrew 1 Liu, Huaping ...and 87 more Authors all top 5 Cited in 20 Serials 11 Statistical Applications in Genetics and Molecular Biology 11 The Annals of Applied Statistics 5 Journal of Agricultural, Biological, and Environmental Statistics 4 Methods in Molecular Biology 2 Biometrics 2 Journal of the American Statistical Association 2 Bayesian Analysis 1 Statistics & Probability Letters 1 Journal of Applied Statistics 1 Biostatistics 1 Statistical Modelling 1 Statistical Methods and Applications 1 Journal of the Korean Statistical Society 1 Computational & Mathematical Methods in Medicine 1 Electronic Journal of Statistics 1 Journal of Probability and Statistics 1 Journal of Theoretical Biology 1 ICSA Book Series in Statistics 1 Frontiers in Probability and the Statistical Sciences 1 Chapman & Hall/CRC Computational Biology Series all top 5 Cited in 6 Fields 43 Statistics (62-XX) 35 Biology and other natural sciences (92-XX) 3 General and overarching topics; collections (00-XX) 2 Numerical analysis (65-XX) 1 Probability theory and stochastic processes (60-XX) 1 Computer science (68-XX) Citations by Year