All pull requests

Pull requests

• feat: add WNN

  #4428·Intron7 opened Oct 21, 2026Member·

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  1

• perf: sample discarded counts in downsample_counts when keeping most of the data

  #4427·carlosvega opened Oct 21, 2026·4 tasks done·

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  1

• perf: numba kernels for pp.harmony_integrate

  #4424·timtreis opened Oct 17, 2026Member·

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  3

• fix: symmetric gauss connectivities for pynndescent / sparse distances

  #4423·syahra712 opened Oct 16, 2026·3 of 5 tasks·

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• fix: downsample_counts precision for float32 data above 2**24 counts

  #4422·syahra712 opened Oct 16, 2026·3 of 5 tasks·

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• fix: keep infinite normalized dispersions in n_top_genes cutoff

  #4419·jorgoose opened Oct 13, 2026·4 of 5 tasks·

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  3

• docs: clarify supported file names in read_10x_mtx docstring (#2128)

  #4418·thirumurugan-2006 opened Oct 13, 2026·3 of 6 tasks·

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• Fix highly variable gene selection with duplicate names

  #4417·thirumurugan-2006 opened Oct 12, 2026·5 tasks done·

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• feat(archetype): add archetype projection

  #4412·SupaNautilus opened Oct 10, 2026·

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• fix: respect n_top_genes with duplicate variable names

  #4409·benjaminkramer510 opened Oct 9, 2026·4 tasks done·

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• fix: downsample_counts(total_counts=...) silently did nothing for Fortran-ordered dense X

  #4408·entity-0-0-2 opened Oct 9, 2026·2 of 3 tasks·

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• fix: handle zero counts in Pearson residual normalization

  #4404·HamzaAhmed-bio opened Oct 8, 2026·2 tasks done·

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• docs: clarify var_names lookup when gene_symbols is set

  #4402·cpruijsen opened Oct 7, 2026·2 of 3 tasks·

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• Fix Ingest truncating to settings.N_PCS even when pp.neighbors used more PCs

  #4401·SID-6921 opened Oct 7, 2026·

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• Zb/markers de api

  #4400·zboldyga opened Oct 6, 2026Contributor·2 tasks·

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• perf: avoid dense BasePlot aggregation

  #4399·srikarjy opened Oct 3, 2026·2 of 3 tasks·

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• fix: stabilize regress_out for ill-conditioned covariates

  #4388·Silas-Zeng opened Sep 29, 2026·

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  · 1.12.5
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• fix: multi-column groupby crashing on non-string observations

  #4385·barlowa124 opened Sep 28, 2026·

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  · 1.12.5
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  4

• fix: honor user-supplied hue in sc.pl.violin

  #4383·barlowa124 opened Sep 28, 2026·2 tasks done·

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• feat: add poisson_gene_selection flavor to pp.highly_variable_genes

  #4379·Sizerta opened Sep 26, 2026·3 tasks done·

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• feat: sample score_genes controls per gene

  #4373·Sizerta opened Sep 21, 2026·2 tasks done·

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  4

• fix: keep gene order in batched highly_variable_genes without n_top_genes

  #4371·haeganm opened Sep 17, 2026·2 of 3 tasks·

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  · 1.12.5
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  1

• fix: reject mismatched raw var names in QC metrics

  #4364·AkshajKashyap opened Sep 13, 2026·2 of 3 tasks·

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• feat: switch to use and out

  #4359·flying-sheep opened Sep 11, 2026Member·6 of 8 tasks·

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  · 1.13.0
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  33

• fix: correct binary logistic marker score direction

  #4348·dnncha opened Sep 8, 2026·

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  · 1.12.5
  6