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Drugs, BeatAML, CanSMILES Updates#252

Merged
jjacobson95 merged 21 commits intomainfrom
drop_drugs
Dec 6, 2024
Merged

Drugs, BeatAML, CanSMILES Updates#252
jjacobson95 merged 21 commits intomainfrom
drop_drugs

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@jjacobson95 jjacobson95 commented Nov 22, 2024

This PR will do the following:

  • Drop Problematic Drugs,
  • Switch BeatAML to Synapse download
  • Switch BeatAML to use canSMILES instead of IsoSmiles for improve_sample_id mapping.
  • Drop IsoSMILES from All datasets.

This resolves #241, #248, and #249.

Update:
This also resolves a new bug relating to the GDC tool update (#254) as well as previously missed NCI60 one (#253).

@sgosline I'm going to merge your MPNST PDX branch into this branch, and rebuild with that. Once that runs to completion successfully, we can merge to main.

@jjacobson95 jjacobson95 merged commit f2120e4 into main Dec 6, 2024
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remove drugs from CTRP dataset

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