eddings / bicoverlapper

Gene Expression Visualization Tool

To run the code:

1. Include all .jar in the lib folder in the project (some of them might not be necessary, but most all. Anyways, it needs a bit of cleaning)

2. Use VM arguments as follows: -Xmx1024m -d32 -Xrs -Djava.library.path="/Library/Frameworks/R.framework/Resources/library/rJava/jri" (-Djava.library.path must point to the jri folder of the rJava package installed in R) (-d32 is only necessary in 64 bit machines)

3. Add the enrivonment variable R_HOME pointing to the install folder of R (where the lib, bin, etc. are located). For example, in the case of Max OS 10.6, this uses to be /Library/Frameworks/R.framework/Resources

4. Note that several R/Bioconductor packages must be installed in order to get all the functionality of BicOverlapper:

   From R: rJava, XML

   From BioConductor: annotate, GO.db, GOstats - for gene annotation biomaRt - for gene annotation biclust, limma, isa2, GSEAlm - for analysis ArrayExpress, GEOquery - for experiment download (NOTE: GEOquery may require curl) Platform annotation packages - for specific platforms (e.g hgu133v2.db or org.Sc.sgd.db)