SignatureAnalysis-CaseStudy

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.