DCeN

Dynamically Co-expressed Neighborhoods (DCeN)

The dcen R-package implements the Dynamically Co-expressed Neighborhoods (DCeN) for ranking genes in genome-wide time-resolved gene expression profiling studies.

Installation

Before installing dcen, you need to have R. For the installation of R, please refer to the R project website (http://cran.r-project.org/). Download the dcen package from the links below. Linux users can install dcen from the source by typing at the directory where the file is saved:
R CMD INSTALL dcen_1.0.0.tar.gz
Windows users may use the ‘Install package(s) from local zip files …’ option in the Packages menu of the R-GUI to browse and install the pre-compiled dcen package.

Download

Package source: dcen_1.0.0.tar.gz
Windows binary: dcen_1.0.0.zip
R-documentation: dcen_1.0.0.pdf

The dcen R-packages are made available under the terms of the GNU General Public License, which means that the source code is freely available for use within other software, but if you alter the code and distribute it, you must make the new source code freely available as well. This software is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY. In case you use the package in your work, we appreciate a citation to our DCeN publication.

Citation

L. L. Elo and B. Schwikowski (2013) Analysis of Time-Resolved Gene Expression Measurements Across Individuals. PLoS ONE 8(12): e82340.

Usage

library(dcen)
dcen.out <- dcen(data1, data2 , filter.p=0.05, filter.n=0.25)

More details about the package and its usage can be found from the R-documentation, which is included in the distribution of the dcen R-package, and can be displayed in R by typing:
help(dcen)
If you experience a problem or bug, please contact us.

Author

Laura L. Elo