I installed cmapPy but I don't know how to use it to read gctx files. I read the documentation. If anyone knows how to do it with cmapPy or any faster method your help would be greatly appreciated. I don't know a lot about this stuff so sorry for the nonspecificity of the question.

  • $\begingroup$ Hi @Bluebells you question is perfectly fine. Could you explain your project please? $\endgroup$
    – M__
    Nov 11 '20 at 22:45
  • $\begingroup$ @Michael There is no project, I'm not even an academic otherwise I could just use clue.io. I'm just interested in seeing how results from GWA studies might be used for drug repurposing. I've been using cmap in conjunction with predixcan. I've been experimenting a lot with gene expression signatures and how they might translate into therapeutic candidates. Up until now I was using a previous dataset on broadinstitute.org/cmap but the site is down, probably forever.It's a hobby I guess. $\endgroup$
    – blue bells
    Nov 11 '20 at 22:59
  • $\begingroup$ Okay thats clearer thanks. Using metadata matrix manipulation interfaced with GWA. Its written in Python2 ... that is a headache and its not a good sign. $\endgroup$
    – M__
    Nov 11 '20 at 23:06

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