This repository is for reproducing the results of a case study in the ADAGE signature analysis paper.
The ADAGE signature analysis was performed in R using the ADAGEpath package. We also performed the GSEA analysis as a comparison.
Here are the steps to repeat the analysis:
- Clone this repository.
- Install the R packages readr, DT, knitr, VennDiagram from CRAN.
install.packages("devtools")
devtools::install_cran(c("readr", "DT", "knitr", "VennDiagram"))- Install ADAGEpath from github.
devtools::install_github("greenelab/ADAGEpath")- Download the GSEA java program from http://software.broadinstitute.org/gsea/downloads.jsp and put it in the repository folder.
- Knit case-study.Rmd in RStudio.