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Update cell line data to use orcestra-downloader #287

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sgosline opened this issue Jan 3, 2025 · 1 comment
Open

Update cell line data to use orcestra-downloader #287

sgosline opened this issue Jan 3, 2025 · 1 comment
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enhancement New feature or request

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@sgosline
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sgosline commented Jan 3, 2025

There is a python-based way to access the cell line drug data here: https://github.com/bhklab/orcestra-downloader

This could help address the reduction in image size for #230 .

@jjacobson95
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Just a note - I looked into this package and all of the files are downloaded as RDS files. We can use pyreadr in python to load these in directly as pandas dataframes without needing R installed. This would be a pretty significant overhaul of the current code we use to download our cell lines but certainly doable.

NCI60 is included as well, so this could be joined in directly rather than a separate step.

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