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Fixing metrics access #19

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Fixing metrics access #19

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6546f85
Update pandas syntax when accessing metrics
mumichae Dec 19, 2023
a91a841
Merge branch 'Teichlab:master' into mumichae-patch-1
mumichae Jun 9, 2025
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8 changes: 4 additions & 4 deletions sctk/_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -508,10 +508,10 @@ def cellwise_qc(adata, metrics=None, cell_qc_key="cell_passed_qc", uns_qc_key="s
"No cells passed. Performing simple filtering on counts, genes and mito%"
)
adata.obs[cell_qc_key] = (
(adata.obs.n_counts >= metrics["n_counts"][0])
& (adata.obs.n_genes >= metrics["n_genes"][0])
& (adata.obs.percent_mito < metrics["percent_mito"][1])
)
(adata.obs.n_counts >= metrics.loc["n_counts", "min"])
& (adata.obs.n_genes >= metrics.loc["n_genes", "min"])
& (adata.obs.percent_mito < metrics.loc["percent_mito", "max"])
)


def filter_qc_outlier_legacy(
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