mseq: Modeling non-uniformity in short-read rates in RNA-Seq data

This package implements all the methods in the paper "Modeling non-uniformity in short-read rates in RNA-Seq data". Especially, it implements both the iterative glm procedure for the Poisson linear model and the training procedure of the MART model. The cross-validation for both of the methods is also implemented. Version 1.1 and later also implements the Poisson linear model with dinucleotide composition. Version 1.2 corrected a bug in expData.R. This bug leads to mis-labeled lines in plotCoef.R, but will not change other parts like training, testing, or cross-validation.

Version: 1.2
Depends: R (≥ 2.5), gbm
Published: 2011-09-08
Author: Jun Li
Maintainer: Jun Li <junli07 at>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] (see file LICENSE)
NeedsCompilation: no
CRAN checks: mseq results


Reference manual: mseq.pdf
Package source: mseq_1.2.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
OS X Snow Leopard binaries: r-release: mseq_1.2.tgz, r-oldrel: mseq_1.2.tgz
OS X Mavericks binaries: r-release: mseq_1.2.tgz
Old sources: mseq archive

Reverse dependencies:

Reverse depends: lmbc