Voom swMATH ID: 14009 Software Authors: Law, C. W., Chen, Y., Shi, W., Smyth, G. K. Description: Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments. The voom method estimates the mean-variance relationship of the log-counts, generates a precision weight for each observation and enters these into the limma empirical Bayes analysis pipeline. This opens access for RNA-seq analysts to a large body of methodology developed for microarrays. Simulation studies show that voom performs as well or better than count-based RNA-seq methods even when the data are generated according to the assumptions of the earlier methods. Two case studies illustrate the use of linear modeling and gene set testing methods. Homepage: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053721/ Related Software: edgeR; Bioconductor; R; limma; DEseq; DESeq2; BaySeq; CRAN; ShrinkBayes; gcrma; TopHat; QuasiSeq; Salmon; RSEM; Phyloseq; ggplot2; RUVseq; DEGseq; diffHic; csaw Cited in: 18 Publications all top 5 Cited by 51 Authors 2 Nettleton, Dan 2 Smyth, Gordon K. 1 Alexander, Warren S. 1 Bonafede, Elisabetta 1 Celeux, Gilles 1 Cheng, Ruihua 1 Cornwell, Steffen 1 Corrada Bravo, Héctor 1 Gallopin, Mélina 1 Gunady, Mohamed K. 1 Ibrahim, Joseph George 1 Jaffrézic, Florence 1 Jia, Gaoxiang 1 Jin, Chong 1 Johnson, Marla 1 Lee, Stanley 1 Li, Qiwei 1 Liang, Kun 1 Lithio, Andrew 1 Liu, Fangfang 1 Liu, Haibo 1 Lu, Wei 1 Lun, Aaron T. L. 1 Majewski, Ian J. 1 Martin, Bryan D. 1 Mount, Stephen M. 1 Nguyen, Yet Tien 1 Phipson, Belinda 1 Picard, Franck 1 Purdom, Elizabeth 1 Rau, Andrea 1 Robin, Stéphane 1 Ruddy, Sean 1 Signorelli, Mirko 1 Spitali, Pietro 1 Sun, Wei 1 Tang, Ximing 1 Tsonaka, Roula 1 Tuggle, Christopher K. 1 Viroli, Cinzia 1 Wang, Chong 1 Wang, Xinlei 1 Wei, Zhi 1 Willis, Amy D. 1 Wilson, Douglas R. 1 Wistuba, Ignacio 1 Witten, Daniela M. 1 Wolff, Alexander 1 Xia, Yinglin 1 Xie, Yang 1 Zhou, Yihui all top 5 Cited in 7 Serials 6 The Annals of Applied Statistics 3 Journal of Agricultural, Biological, and Environmental Statistics 2 Biometrics 2 Statistical Applications in Genetics and Molecular Biology 1 Journal of the American Statistical Association 1 Statistical Modelling 1 ICSA Book Series in Statistics Cited in 2 Fields 16 Statistics (62-XX) 14 Biology and other natural sciences (92-XX) Citations by Year