The Benfey Lab runs a publicly accessible Maven repository. For each published Java application or library, this repository contains the license agreement, executable jar file, javadoc, and source code. A human-accessible interface for this repository is located at Benfey Lab Maven Repository. The primary goal of this repository, however, is to provide programmatic access to published Java software.
A human-oriented website is located at Benfey Lab Software. It provides documentation for published software and links to the Maven repository where files can be downloaded.
This software can be used to identify the biological significance of genes associated with dominant expression patterns. This software is used to identify statistically significant enriched Gene Ontology (GO) categories, transcription factor families, and biological processes that have been identified via microarray analysis.
ChipEnrich is distributed as an executable
To run it, you need
Java Runtime Environment (JRE)
version 1.5 or later.
When you have JRE installed and
Dominant Pattern Identification (DPI)
This software was used in Brady et al., 2007. A detailed description of Dominant Pattern Identification software, including the method used and input files structure, is given in Orlando et al., 2008.
DPI software is distributed as Perl script. The Perl script communicates to the user to obtain required parameters (input and output file names, modes, etc.) and generates an R program. The generated R program can be later executed on the user's computer or submitted for execution to a cluster of computers.
The Perl script provides extensive help and does not perform any non-reversable action without explicit confirmation from the user. -- So, it is safe to run the Perl script to learn more about this software.
To run DPI software, one needs:
To install DPI software on your computer:
To run DPI software on your computer:
You can rename the Perl script to use shorter name if you prefer.