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Pull requests: scverse/scanpy

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Pull requests list

feat: pydantic settings
#4081 opened Apr 21, 2026 by flying-sheep Member • Draft
3 tasks
docs: clarify method vs transformer in sc.pp.neighbors
#4079 opened Apr 21, 2026 by CuiweiG Loading… 1.12.2
1
3
docs: add inline example plot to sc.pl.scatter
#4078 opened Apr 21, 2026 by CuiweiG Loading…
1
WIP base without X_
#4076 opened Apr 20, 2026 by flying-sheep Member • Draft
3 tasks
1
Optimize sparse matrix aggregation and conversion handling
#4073 opened Apr 17, 2026 by mumichae Contributor Loading…
3 tasks done
1
3
feat: add layer argument to 10x read functions
#4072 opened Apr 17, 2026 by flying-sheep Member • Draft
1 of 3 tasks
1
1
perf: Combat perf improvements
#4070 opened Apr 17, 2026 by ilaykav Loading…
2 of 3 tasks
1.12.2
2
feat: add illicofor rank_genes_groups
#4038 opened Apr 7, 2026 by ilan-gold Contributor • Draft
6 of 7 tasks
22
feat: allow exponentiation post agg for log-fold-change in rank_genes_groups Area – Reproducibility Exact replication
#4037 opened Apr 7, 2026 by ilan-gold Contributor Loading…
1 of 3 tasks
1.13.0
1
@ilan-gold
13
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
feat: add Harmony to scanpy
#3953 opened Jan 26, 2026 by Intron7 Member Loading… 1.13.0
1
@flying-sheep @Intron7 @ilan-gold
12
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
chore(deps): bump actions/upload-artifact from 5 to 6 dependencies Pull requests that update a dependency file github_actions Pull requests that update GitHub Actions code
#3913 opened Dec 15, 2025 by dependabot Bot Loading…
2
Add ncols parameter to pl.violin()
#3912 opened Dec 11, 2025 by LoganLarlham Loading…
Add values_to_plot support to matrixplot and heatmap (issue #3842)
#3902 opened Nov 25, 2025 by giovanamotta • Draft
1
1
Custom neighbor transformers with varying neighbor count and respect knn
#3807 opened Sep 19, 2025 by maltekuehl Contributor • Draft
2 of 3 tasks
2
1
Refactor BasePlot: avoid unnecessary DataFrame conversion
#3765 opened Aug 17, 2025 by etching-7z • Draft
3 tasks
performance: Refactor BasePlot & subclasses to copy less
#3757 opened Aug 3, 2025 by dorzhey Loading…
3 tasks done
1.13.0
3
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