opm package for
R is a
comprehensive software for analysing phenotype microarray and
growth-curve data. For more information, see the
opm page at DSMZ or the
main tutorial for
The package can be used on Windows, Mac and Linux/UNIX
systems. As a prerequisite, one needs to obtain the statistical
R. We also recommend
a graphical user interface such as RStudio. Both are freely available;
instructions for installation are given on their websites. Maria
del Carmen Montero-Calasanz has compiled a detailed description of
the installation of
opm etc. under Windows. The
shown use of graphical user interfaces is similar on other
There are three ways to install
opm and its
dependencies. The first way is to visit the
R-Forge site, download the source files or Windows binaries
and install them locally. Alternatively, at the
You will then be asked for what exactly to install. In our
experience this works well under Windows, if otherwise please let
us know. (But please first see the troubleshooting section.)
opm and its helper packages can be downloaded
using the links further below on this page and installed manually
(and optionally checked beforehand). Documentation comes with the
packages but is also linked below.
The only somewhat more frequently encountered problems we are
aware of when attempting to install
opm and its
dependencies are the following.
R. Detailed instructions on how to do this are given elsewhere.
Rpackages on which
opmor the installation script depend hinder the installation. To solve this we recommend biocLite as a convenient tool to install not only
Bioconductorbut also core packages, and to update many packages at once. To use
biocLitejust copy and paste the code snippet shown there into the
Rtoolsis not needed to install the
opmpackage (not even under Windows), but we have observed that old
Rtoolsversions might yield errors with the
opminstallation script. If so, either deinstall or upgrade
Rtoolsbefore running the script.
In the case of errors that cannot be resolved, please send us the complete output generated when loading the installation file.
||the main tutorial for
|Substrate information in
||availability and use of data on phenotype microarray
|Growth curves in
|pkgutils||comprehensive online documentation of the latest
|opm||comprehensive online documentation of the latest
|opmdata||comprehensive online documentation of the latest
|opmextra||comprehensive online documentation of the latest
|RStudio||notes on the use of
|pkgutils||built and checked
|opm||built and checked
|opmdata||built and checked
|opmextra||built and checked
The last change to the packages or their documentation has been made on Mon Nov 14 14:03:15 CET 2016.
We thank the authors and maintainers of the
packages on which
opmdata depend and of those packages used to
generate this documentation. Helpful feedback from
opm users is gratefully acknowledged.
||Lea A.I. Vaas, J. Sikorski, B. Hofner, N. Buddruhs, A. Fiebig, H.-P. Klenk and M. Göker. "opm: An R package for analysing OmniLog® Phenotype MicroArray Data". Bioinformatics 29 (14): 1823-1824, 2013.|
|Parameter comparison and visualization with
||Lea A.I. Vaas, J. Sikorski, V. Michael, M. Göker and H.-P. Klenk. "Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics". PLoS ONE 7 (4): e34846, 2012.|
|Advanced usage of
||B. Hofner, L. Boccuto and M. Göker. "Controlling false discoveries in high-dimensional situations: Boosting with stability selection". BMC Bioinformatics 16 (6): 144, 2015.|
opmdata packages are free software published under
the GPL and
come with absolutely no warranty. This holds even though a lot of
effort was invested into getting the packages free of bugs.
For contact addresses see the
opm page at DSMZ.