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Regenerate or move wilms-06 module exploratory CNV notebooks #875

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sjspielman opened this issue Nov 12, 2024 · 1 comment
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Regenerate or move wilms-06 module exploratory CNV notebooks #875

sjspielman opened this issue Nov 12, 2024 · 1 comment
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@sjspielman
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sjspielman commented Nov 12, 2024

This PR issue tracks updating the copyKAT and inferCNV exploratory notebooks in the cell-type-wilms-tumor-06 module, once code being developed towards #810 has been completed and merged into main.

See here for some additional context: #873 (comment)

I cannot fully render these notebooks (though I confirmed they run with test data!) due to compute limitations, so I see these as the best two ways to handle them:

  • We can actually potentially remove these notebooks from the repo and send them to results instead, since they are not part of the actual annotation pipeline. In this case, I would take those steps in the third PR.
  • We can probably ask Maud to regenerate these notebooks once we merge all this code into main. In this case, I would file an issue for followup.
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Closing in favor of #906

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