Here is a knitr-powered report, including code, to reproduce all the results in the manuscript, Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery.

• Drug repositioning for psoriasis based on cogena.pdf shows all the code and results related with GSE13355.
• src contains the Rmd files to generate the two pdf files above, the WGCNA-pathway analysis of the dataset GSE13355.
• data is used to store the raw data from GEO.
• results contains the the input and output of GSEA, CMap, NFFinder and WGCNA.
• tmp is to store the temporary file.

cogena package is available at Bioconductor or my Github.

Citation: Jia, Zhilong, et al. "Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery." BMC Genomics 17.1 (2016): 1.