I'm having little success accessing the data behind the clue.io CMAP Touchstone web-based application.
To be clear, Touchstone is the [-100:100] scored pair-wise comparison between a drug of interest, and all other available drugs in the dataset. It does not return transcript signatures (which yield z-scores of [-10,10] - the collapsed z-score's of N-repeats of a particular compound can be downloaded from www.clue.io->Data Library->Touchstone Reference Dataset->GSE92742_Broad_LINCS_Level5_COMPZ.MODZ_n473647x12328.gctx.gz).
The clue.io provides an API but that's only for signature based queries e.g., upload your list of up/down regulated gene and see what drugs match). Equally, the L1000FWD also returns signature values only.
A round-about way of getting this data would be to use the diff gene signature of your drug of interest as the input back into the clue.io API. However, this would return all the cell lines, doses and exposure times and would require significant post processing. I don't want to reinvent the wheel given that the web-based Touchstone application will do this for me.
I can imagine there is a scored pert_id x pert_id matrix gctx file, but I'm unable to locate one.
Any suggestions? Thanks.
If you are not able to use the API provided by
clue.iothen you may want to contact their support with this question.Indeed I did. 7 days and I'm yet to hear from them. I was hoping, a member of the wider community might have an answer.