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min_cells argument to load_and_normalize() - #28

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jjschirle merged 1 commit into
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min_cells
Sep 3, 2026
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min_cells argument to load_and_normalize()#28
jjschirle merged 1 commit into
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min_cells

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Adding min_cells argument to load_and_normalize(). This filters out genes that are not uniquely expressed in at least (<) min_cells cells.

Note: This is different than gene_threshold, which filters genes based on total raw counts across cells.

Intended as a quick patch, future development should integrate this functionality within an object-oriented ecosystem. One could envision a future variant of load_and_normalize() with the following functionality:

Parameter/concept Filters Criterion
min_cell_counts cells total counts in the cell
min_genes cells number of genes detected in the cell
gene_threshold genes total expression/counts across cells
min_cells genes number of cells where gene is detected

@jjschirle
jjschirle requested a review from aarmey September 3, 2026 20:29
@jjschirle
jjschirle merged commit eafde96 into main Sep 3, 2026
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@aarmey
aarmey deleted the min_cells branch September 4, 2026 12:44
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2 participants