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