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limma Linear Models for Microarray and RNA-Seq Data User’s ...
Guide, see for example Section 8.2 and the E. coli and estrogen case studies. Functions for reading and pre-processing expression data from Illumina BeadChips were intro-duced in limma 3.0.0. See the case study in Section 17.3 for an example of these. Limma can also be
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Package ‘wateRmelon’ - Bioconductor - Home
www.bioconductor.orgPackage ‘wateRmelon’ November 17, 2018 Type Package Title Illumina 450 methylation array normalization and metrics Version 1.26.0 Author Leonard C Schalkwyk, Ruth Pidsley, Chloe CY Wong, with functions con-
limma Linear Models for Microarray and RNA-Seq Data …
www.bioconductor.orgChapter 1 Introduction Limma is a package for the analysis of gene expression data arising from microarray or RNA-seq technologies [32]. A core capability is the use of linear models to assess di erential expression in
DESeq2: Differential gene expression analysis based on the ...
www.bioconductor.orgPackage ‘DESeq2’ January 20, 2022 Type Package Title Differential gene expression analysis based on the negative binomial distribution Version 1.34.0
edgeR: differential analysis of sequence read count data ...
www.bioconductor.org2.15Gene set testing.....25 2.16Clustering, heatmaps etc ... MD, and Smyth, GK (2008). Small sample estimation of negative binomial dis-persion,withapplicationstoSAGEdata. Biostatistics 9,321–332. ... All other questions or problems concerning edgeR should be …
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