rmRNAseq: RNA-Seq Analysis for Repeated-Measures Data

A differential expression analysis method for RNA-seq data from repeated-measures design using general linear model framework and parametric bootstrap inference. The method accounts for the dependence of gene expression levels due to the repeated-measures through continuous autoregressive correlation structure. The method is described in Chapter 4 of Nguyen (2018) <https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=7433&context=etd>.

Version: 0.1.0
Depends: R (≥ 3.3)
Imports: AUC (≥ 0.3.0), Biobase, DESeq2, edgeR (≥ 3.16.5), graphics, limma (≥ 3.30.13), MASS (≥ 7.3-45), Matrix (≥ 1.2-8), methods, nlme (≥ 3.1-131), parallel, reshape (≥ 0.8.6), rlang, splines, splineTimeR, statmod (≥ 1.4.29), stats
Suggests: knitr, rmarkdown, testthat
Published: 2019-11-08
Author: Yet Nguyen [aut, cre], Dan Nettleton [aut], Charity Gordon Law Smyth [ctb] (The authors of limma::voom, which was modified slightly leading to my_voom), Agata Michna [ctb] (The author of splineTimeR::splineDiffExprs, which was modified slightly leading to my_splineDiffExprs)
Maintainer: Yet Nguyen <tienyettoan at gmail.com>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
Materials: README
CRAN checks: rmRNAseq results

Downloads:

Reference manual: rmRNAseq.pdf
Package source: rmRNAseq_0.1.0.tar.gz
Windows binaries: r-devel: rmRNAseq_0.1.0.zip, r-devel-gcc8: rmRNAseq_0.1.0.zip, r-release: rmRNAseq_0.1.0.zip, r-oldrel: rmRNAseq_0.1.0.zip
OS X binaries: r-release: not available, r-oldrel: not available

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