opm: Analysing Phenotype Microarray and Growth Curve Data

Tools for analysing OmniLog(R) and MicroStation(TM) phenotype microarray (PM) data as produced by the devices distributed by BIOLOG Inc. as well as similar kinds of data such as growth curves. Major facilities are plotting data, accurately estimating curve parameters, comparing and discretising data, creating phylogenetic formats and reports for taxonomic journals, drawing the PM analysis results in biochemical pathway graphs optionally including genome annotations, running multiple comparisons of means, easy interaction with powerful feature-selection approaches, integrating metadata, using the YAML format for the storage of data and metadata, batch conversion of large numbers of files, and database I/O. (The suggested mboostDevel is from R-Forge and not necessary.)

Version: 1.1.0
Depends: R (≥ 3.0.0)
Imports: methods, lattice, parallel, boot, hwriter, plotrix, Ckmeans.1d.dp, pkgutils (≥ 0.6.0), yaml (≥ 2.1.7), splines, mgcv, grofit (≥ 1.1), rjson (≥ 0.2.12), nlme, DBI
Suggests: optparse, gplots, opmdata (≥ 0.4.0), testthat, multcomp, KEGGREST, pathview, mboostDevel (≥ 2.3.0), gridExtra
Published: 2014-04-22
Author: Markus Goeker, with contributions by Benjamin Hofner, Lea A.I. Vaas, Johannes Sikorski, Nora Buddruhs and Anne Fiebig
Maintainer: Markus Goeker <markus.goeker at dsmz.de>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: http://opm.dsmz.de/
NeedsCompilation: no
Citation: opm citation info
Materials: NEWS ChangeLog
CRAN checks: opm results

Downloads:

Reference manual: opm.pdf
Vignettes: Growth curves in opm
Substrate information in opm
Using opm
Package source: opm_1.1.0.tar.gz
OS X binary: opm_1.0.24.tgz
Windows binary: opm_1.1.0.zip
Old sources: opm archive

Reverse dependencies:

Reverse depends: opmdata