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Optimize depmap driver analysis #37

Merged
merged 38 commits into from
Oct 26, 2023
Merged

Optimize depmap driver analysis #37

merged 38 commits into from
Oct 26, 2023

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johnurbanik
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What?

  • add process.py which is used for depmap driver analysis
  • add proxbias/notebooks/DepMap_PB_Driver_Analysis.ipynb and proxbias/notebooks/DepMap_PB_Sample.ipynb to include analysis performed and sample of how to use driver code
  • add optimized versions of monte carlo simulation code that utilize numba
  • add csv for cancer gene list
  • reorganize repo to make things more clear
  • make downloading depmap rnai data optional to speed up usage
  • clean up .gitignore for public release
  • update dependencies

Why?

  • all code is necessary for public release or related to reviewer comments.

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nathanlazar
nathanlazar previously approved these changes Oct 26, 2023
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@nathanlazar nathanlazar left a comment

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Thank you!

Some of the functions could use better doc strings, but I'm going to add another notebook to generate the new box & scatter plots so I can do that on that PR.
in depmap/process:

  • split_models the behavior isn't really obvious from the code, so a doc string with a description would be good.
  • Docstring for bootstrap_stats is just a list of parameters

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Looks great, thanks!

@johnurbanik johnurbanik merged commit ce2cddd into trunk Oct 26, 2023
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@johnurbanik johnurbanik deleted the depdriver branch October 26, 2023 15:13
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2 participants