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.