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This R script can be applied to parse the GCT or GCTX files by using the cmapR package.
Source of CMAP-LINCS GCTX file:
GSE92742 - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92742
GSE70138 - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70138
GSE92743 - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92743
Date: 3/8/2018
Author: Jeff