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Create util script to convert the NBAtlas cell type metadata #1175

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sjspielman opened this issue Jun 16, 2025 · 0 comments
Open

Create util script to convert the NBAtlas cell type metadata #1175

sjspielman opened this issue Jun 16, 2025 · 0 comments
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If you are filing this issue based on a specific GitHub Discussion, please link to the relevant Discussion.

Part of #1151

Describe the goals of the changes to the analysis module.

We plan to reformat the NBAtlas tumor metadata we received for input to this module. Rather than a data frame object, we'd like this to be a plain text file of cell ids.

What will your pull request contain?

Small helper script for posterity, in a separate scripts/setup folder. As of now, we would not want this script to be run in CI, and its documentation should explain that it's only used for an initial conversion. Note that this would have to change if the metadata we're using ends up being public at some point, but that is not our call.

Will you require additional software beyond what is already in the analysis module?

No

Will you require different computational resources beyond what the analysis module already uses?

No

If known, when do you expect to file the pull request?

This sprint

@sjspielman sjspielman self-assigned this Jun 16, 2025
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