ATAC QC component #868
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ATAC QC component #868
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DriesSchaumont
requested changes
Oct 4, 2024
| mdata = mu.read(par["input"]) | ||
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| logger.debug("Making var names unique") | ||
| mdata.var_names_make_unique() |
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I think I want to avoid calling this here
| atac.obs.drop(col, axis=1, inplace=True) | ||
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| logger.info("Calculating QC metrics") | ||
| sc.pp.calculate_qc_metrics(atac, percent_top=None, log1p=False, inplace=True, layer=par["layer"]) |
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I want to avoid that things get overwritten by scanpy, could you pass a copy of the data?
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Did it manually
Co-authored-by: Dries Schaumont <[email protected]>
Co-authored-by: Dries Schaumont <[email protected]>
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Tests are now failing due to incorrect scanpy version specification: Shouldn't be a problem on my side, I just use |
DriesSchaumont
requested changes
Dec 4, 2024
Co-authored-by: Dries Schaumont <[email protected]>
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Changelog
Add component for calculating QC metrics for ATAC data.
Issue ticket number and link
Contributes to #398
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I have performed a self-review of my code
Conforms to the Contributor's guide
Check the correct box. Does this PR contain:
Proposed changes are described in the CHANGELOG.md
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