Add ComBat-Seq method #55
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NB: waiting on approval to run the CI workflow. |
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@EpigeneMax Could you update your branch to the latest main commit? |
Done. |
mumichae
requested changes
Aug 29, 2025
mumichae
reviewed
Sep 25, 2025
mumichae
reviewed
Sep 25, 2025
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| print("Read input", flush=True) | ||
| adata = read_anndata( | ||
| par["input"], X="layers/normalized", obs="obs", var="var", uns="uns" |
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@rcannood Could you confirm if this is the correct way to read the counts layer, given that preferred_normalization: counts. I haven't seen any example where preferred_normalization is accessed in the script
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Once it's confirmed that the counts are read correctly, this method can be merged |
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Describe your changes
This PR adds a ComBat-Seq component, based on inmoose implementation.
ComBat-Seq is a state-of-the-art tool for batch correction in bulk RNA-Seq data.
It draws inspiration from ComBat algorithm and adapts it to RNA-Seq.
ComBat is already integrated as a component on this task, adding ComBat-Seq seems quite legitimate.
Checklist before requesting a review
I have performed a self-review of my code
Check the correct box. Does this PR contain:
Proposed changes are described in the CHANGELOG.md
CI Tests succeed and look good!