All pull requests

Pull requests

• feat: sample score_genes controls per gene

  #4373·Sizerta opened Sep 21, 2026·

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  1

  1

• fix: keep gene order in batched highly_variable_genes without n_top_genes

  #4371·haeganm opened Sep 17, 2026·

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  1

• fix: reject mismatched raw var names in QC metrics

  #4364·AkshajKashyap opened Sep 13, 2026·

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  1

  1

• feat: switch to use and out

  #4359·flying-sheep opened Sep 11, 2026·

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  · 1.13.0
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  9

• fix: correct binary logistic marker score direction

  #4348·dnncha opened Sep 8, 2026·

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  · 1.12.5
  6

• docs: document the adata.uns['hvg'] output of pp.highly_variable_genes

  #4344·asharaali opened Sep 3, 2026·

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  1

  3

• fix: run t-test on log values regardless of mean_in_log_space

  #4337·cindykrafft opened Sep 2, 2026·

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  1

  1

• fix: handle scalar string groups in ranked-gene plots

  #4330·yingluosanqian opened Aug 31, 2026·

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  2

• fix: keep FlyBase gene nan when reading 10x mtx

  #4329·joncarse opened Aug 29, 2026·

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  1

  4

• feat: add configurable columns to PAGA plots

  #4325·AtomicGlance opened Aug 27, 2026·

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  · 1.13.0
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  7

• fix: sc.pl.paga cax handling with multiple colors

  #4319·AdvaitS opened Aug 22, 2026·

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  1

  1

• feat: Add ncols parameter to pl.paga

  #4317·AdvaitS opened Aug 22, 2026·

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  1

  1

• fix: only warn from log1p when the target representation was already transformed

  #4298·Mohit-Ak opened Aug 16, 2026·

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  1

  2

• docs: document norm parameter for embedding scatter plots

  #4297·Zethson opened Aug 14, 2026·

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  · 1.12.5
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  1

• feat: support acc shortcuts

  #4288·flying-sheep opened Aug 11, 2026·

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  · 1.13.0
  7

  

• Update template to v0.8.0

  #4221·scverse-bot opened Jul 17, 2026·

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  1

• feat: pp.scale allow selecting correction

  #4220·AxelMcKenna opened Jul 16, 2026·

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  2

• feat: add min_cells parameter to dotplot

  #4218·AlsoTheZv3n opened Jul 15, 2026·

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  1

• feat: add Array API support via array-api-compat

  #4179·amalia-k510 opened Jun 25, 2026·

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  · 1.13.0
  40

• feat: add networkit flavor for parallel Leiden clustering

  #4170·amalia-k510 opened Jun 22, 2026·

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  20

• feat(preprocessing): add optimal shifted CLR (PFlog) normalization

  #4160·rwbaber opened Jun 14, 2026·

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  26

• fix(experimental.pp.hvg): scope per-batch clip threshold in pearson_residuals HVG

  Area – Preprocessing 🧼
  #4138·Arshammik opened May 23, 2026·

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  · 1.12.5
  5

• fix: anchor sc.pl.scatter colorbar to user-supplied ax

  #4137·gkneighb opened May 21, 2026·

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  · 1.12.5
  1

  3

• feat: allow precomputed connectivities in neighbors

  #4133·ehsanestaji opened May 19, 2026·

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  · 1.12.5
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  3

• fix: consistent modularity by using Weighted_Adjacency directly

  #4113·flying-sheep opened May 8, 2026·

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  · 2.0.0
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  4