A Python wrapper around GOSeq, a method for performing GO set enrichment on differentially expressed gene sets from RNA-seq experiments.
Check requirements.txt for python requirements. Note that you'll need rpy2, which is non-standard.
On the R Side of the world, you'll need the goseq R package. See: https://bioconductor.org/packages/release/bioc/html/goseq.html for instructions on how to install goseq into your R.
-------------- Running the example command line ---------------------- Make sure you are in the src/ directory then:
For running on Ron's old Trashcan: pwd /Users/Ron/Desktop/GeneSetEnrichment_General/GOSeqPy/src
python runGoSeqRms.py ../goseq_out/ ../ActiveCollaborations/Tattersall/GOSeq_Tattersall/inputData_goseq/TattersallExp2//vaper.post_v_pre/group/all.Up.deSeq2.tsv -pvalcol=5 -pval=0.05 -log2fc=1.5 -log2fccol=2
For running anywhere:
be in the src directory then: python runGoSeqRms.py ../goseq_out/ ../data/all.Up.deSeq2.tsv -pvalcol=5 -pval=0.05 -log2fc=1.5 -log2fccol=2