gsea

Gene set enrichment analysis using Fisher's exact test

####Instructions to use this:

1. add gsea to $PATH

export PATH=$PATH:path_to_gsea/

2. run gsea

gsea file_name background_file_name geneset_name save_name

Here,

file_name is file with test genes (one gene per line)

background_file_name is file with background genes (one gene per line)

geneset_name is filepath+name of a geneset downloaded from msigdb. Need not parse msigdb file. Script takes care of parsing

save_name is filepath+name for output file

Returns the following

test_inset
test_notinset
background_inset
background_notinset
oddsratio
pvalue
bonferroni-adjusted
name of overlapping genes