The scripts for GO, KEGG, and MsigDB hallmark enrichment analyses in batch mode.
The specific workflow is shown in the below.
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For GO and KEGG analyses.
a. Got the relationships between genes and GO/KEGG terms via the Rscript go.update.R and KEGG.update.R.
b. Download the Gene_info data from NCBI (ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/)
c. Run go.enrich.pl or kegg.enrich.pl to obtain the enriched GO/KEGG IDs.
d. Run get.term.pl to map the IDs to terms and descriptions.
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For MsigDB analysis.
a. Download the hallmarks from MsigDB database
b. Run MsigDB.R