To run the code:
- 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)
- Use VM arguments as follows: -Xmx1024m -d64 -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) (-d64 is only necessary in 64 bit machines)
- Add the environment 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
In the case of Debian: -Djava.libary.path="/home/xxx/R/x86_64-pc-linux-gnu-library/3.3/rJava/jri" R_HOME=/usr/lib/R In the case of Debian with anaconda for R: -Djava.library.path="/home/xxx/anaconda3/lib/R/library/rJava/jri" R_HOME=/home/xxx/anaconda3/lib/R
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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 hgu133plus2.db or org.Sc.sgd.db)
For example in Debian+anaconda:
conda install -c bioconda bioconductor-annotate conda install -c bioconda bioconductor-go.db conda install -c bioconda bioconductor-gostats conda install -c bioconda bioconductor-biomart
conda install -c conda-forge r-biclust conda install -c bioconda bioconductor-limma conda install -c bioconda bioconductor-hgu133plus2.db conda install -c bioconda bioconductor-org.sc.sgd.db