Clone the repository and use either devtools::load_all() or devtools::install() to
load the required functions and data. These will install all dependencies as well.
"analysis/00.DownloadPreprocess" directory includes code used to compiled required datasets and some precalculations to speed up the downstream analysis. The output of the "analysis/00.DownloadPreprocess/00.DownloadPreprocess.R" script is already present in this repository therefore this script can be skipped. The rest of the scripts should be run in order to perform the necesarry downloads and pre-processing.
Precalculated results for every step can be found within this repository. These are the instructions to re-generate them from scratch.
'analysis/01.CmapEnrichment' directory contains the code required for running basic cmap enrichment. Running "01.ScoreCalc.R" will populate the "results" directory 'combined.tsv' in this directory includes enrichment score for comparisons.
'analysis/02.L1000Analysis' contains the code required for running comparisons of results using the old CMAP dataset with different forms of the new L1000 dataset. Running these scripts in order will populate respectively named results directories and generate the comparison heatmap.
