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Pull requests: scverse/scanpy

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Pull requests list

Adding "networkit" flavour to scanpy.tl.leiden for parallel community detection
#4170 opened Jun 22, 2026 by amalia-k510 Contributor • Draft
7
feat(preprocessing): add optimal shifted CLR (PFlog1pPF) normalization
#4160 opened Jun 14, 2026 by rwbaber Contributor Loading…
1 of 3 tasks
9
ci: bump codecov/codecov-action from 6 to 7 dependencies Pull requests that update a dependency file github_actions Pull requests that update GitHub Actions code
#4146 opened Jun 8, 2026 by dependabot Bot Loading…
1
perf: chan's parallel mean-var algorithm for dask-backed arrays (sparse/dense) benchmark
#4143 opened Jun 5, 2026 by ilan-gold Contributor Loading…
3 tasks
1.12.2
9
fix(experimental.pp.hvg): scope per-batch clip threshold in pearson_residuals HVG Area – Preprocessing 🧼
#4138 opened May 23, 2026 by Arshammik Loading… 1.12.2
4
fix: anchor sc.pl.scatter colorbar to user-supplied ax
#4137 opened May 21, 2026 by gkneighb Loading… 1.12.2
1
2
feat: allow precomputed connectivities in neighbors
#4133 opened May 19, 2026 by ehsanestaji • Draft
2 of 3 tasks
1.12.2
1
3
feat(plotting): add ncols to wrap multi-panel violin plots (#1552)
#4132 opened May 19, 2026 by Hore01 Contributor Loading…
1
2
Rank refactor 1
#4118 opened May 11, 2026 by zboldyga Contributor • Draft
3 tasks
10
fix: consistent modularity by using Weighted_Adjacency directly
#4113 opened May 8, 2026 by flying-sheep Member • Draft
2 of 3 tasks
2.0.0
1
4
add backends
#4108 opened May 7, 2026 by Intron7 Member • Draft
1
docs: add inline example plot to sc.pl.scatter
#4078 opened Apr 21, 2026 by CuiweiG Contributor Loading…
2
feat: base without X_
#4076 opened Apr 20, 2026 by flying-sheep Member Loading…
2 of 3 tasks
1.13.0
1
3
Optimize sparse matrix aggregation and conversion handling
#4073 opened Apr 17, 2026 by mumichae Contributor Loading…
3 tasks done
1
4
feat: add layer argument to 10x read functions
#4072 opened Apr 17, 2026 by flying-sheep Member • Draft
1 of 3 tasks
1
1
feat: add illicofor rank_genes_groups
#4038 opened Apr 7, 2026 by ilan-gold Contributor Loading…
6 of 7 tasks
1
27
perf: "two-pass" seurat hvg via scanpy.get.aggregate benchmark
#4013 opened Mar 26, 2026 by ilan-gold Contributor • Draft
3 tasks
1.12.2
2
perf: parallel downsample
#4004 opened Mar 18, 2026 by flying-sheep Member • Draft
11
fix: reorder pts/pts_rest to match significance ranking in rank_genes_groups
#3997 opened Mar 10, 2026 by LiudengZhang Contributor Loading…
3 tasks done
1
5
fix: regress_out for more threads than 64
#3954 opened Jan 26, 2026 by Intron7 Member Loading… 1.12.2
3
perf: try out new cliping numba kernel benchmark
#3952 opened Jan 23, 2026 by ilan-gold Contributor • Draft
3 tasks
1.13.0
3
docs: add inline example of pca_variance_ratio
#3950 opened Jan 22, 2026 by marvinbuff Loading… 1.12.2
1
Update template to v0.7.0
#3933 opened Dec 24, 2025 by scverse-bot Loading…
1
Remove "n_genes_by_{expr_type}" typo from variable-level qc metrics docs
#3916 opened Dec 15, 2025 by patcon Loading…
2
chore(deps): bump actions/cache from 4 to 5 dependencies Pull requests that update a dependency file github_actions Pull requests that update GitHub Actions code
#3914 opened Dec 15, 2025 by dependabot Bot Loading…
1
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