PamGeneMixed: Preprocessing and Modeling Kinase Activity Profiles in PamChip Data

This package contains the functions that can be used to analyze the PamChip microarray data. The package is mainly useful in fitting semi-parametric mixed effects models while accommodating various types of mean structures and correlation structures present in Kinase activity profiling experiments. The package can be used to visualize, cleaning Pam Chip data. And also it can be used in model fitting, velocity estimating, and testing the estimated velocities between the groups. The PamGeneMixed package is built up as a software implementation for the paper titled The Use of Semi-parametric Mixed Models to Analyze PamChip Peptide Array Data: an Application to an Oncology Experiment which is published in Bioinformatics (2011).

Version: 1.03
Depends: R (≥ 2.10), mgcv, gplots, utils, graphics, nlme, methods, stats, Biobase
Published: 2013-04-04
Author: Pushpike Thalikarathne, Ziv Shkedy, Dan Lin, Lieven Clement, and Geert Verbeke
Maintainer: Pushpike Thalikarathne <Pushpike at gmail.com>
License: GPL-3
NeedsCompilation: no
Materials: NEWS
CRAN checks: PamGeneMixed results

Downloads:

Reference manual: PamGeneMixed.pdf
Vignettes: An R package for fitting Semiparametric mixed models to Kinase Activity Profiiles
Package source: PamGeneMixed_1.03.tar.gz
Windows binaries: r-devel: PamGeneMixed_1.03.zip, r-release: PamGeneMixed_1.03.zip, r-oldrel: PamGeneMixed_1.03.zip
OS X Snow Leopard binaries: r-release: PamGeneMixed_1.03.tgz, r-oldrel: PamGeneMixed_1.03.tgz
OS X Mavericks binaries: r-release: PamGeneMixed_1.03.tgz
Old sources: PamGeneMixed archive