Files to run the scripts

• CMAP perturbation object:

Run the R scripts

• Fig1a-humanHeatmap.R
• Fig1b-temporalDataClustering&Overrep.R
• Fig2a-PharmaCogenomics.R
• Fig1d-clustering.R

Set up the software environment

R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] PharmacoGx_1.1.6

loaded via a namespace (and not attached):
 [1] igraph_1.0.1        cluster_2.0.4       magrittr_1.5        BiocGenerics_0.14.0 maps_3.1.1          MASS_7.3-45         caTools_1.17.1      tools_3.2.3        
 [9] magicaxis_2.0.0     parallel_3.2.3      Biobase_2.28.0      piano_1.8.2         plotrix_3.6-3       KernSmooth_2.23-15  marray_1.46.0       gtools_3.5.0       
[17] celestial_1.3       digest_0.6.10       lsa_0.73.1          RColorBrewer_1.1-2  mapproj_1.2-4       sets_1.0-16         SnowballC_0.5.1     bitops_1.0-6       
[25] slam_0.1-32         sm_2.2-5.4          limma_3.24.15       gdata_2.17.0        downloader_0.4      relations_0.6-6     gplots_3.0.1        RANN_2.5