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Pull requests: scverse/scanpy

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Pull requests list

Add obsm parameter to normalize_total and pca
#3863 opened Oct 30, 2025 by flying-sheep • Draft
1 of 3 tasks
1
1
ci: fix tests in 1.11 branch
#3860 opened Oct 30, 2025 by flying-sheep Loading…
@flying-sheep
1
Backport PR #3853: fix: scanpy benchmark uses pip for igraph + setup_cache
#3859 opened Oct 30, 2025 by ilan-gold Loading…
1 of 3 tasks
1
Backport PR #3851 on branch 1.11.x (fix: dotplot scaling with swapped axes)
#3856 opened Oct 30, 2025 by meeseeksmachine Loading… 1.11.6
Add jaccard as an additional method in sc.pp.neighbors
#3831 opened Oct 7, 2025 by jpintar Loading…
2 of 3 tasks
1
feat: add n_obs_aggregated column to aggregated AnnData output
#3824 opened Oct 1, 2025 by RohanDisa Loading…
3 tasks done
1.12.0
1
18
Custom neighbor transformers with varying neighbor count and respect knn
#3807 opened Sep 19, 2025 by maltekuehl • Draft
2 of 3 tasks
2
Backport PR #3802 on branch 1.11.x (docs: fix sc.filter_cells return documentation typo)
#3804 opened Sep 18, 2025 by meeseeksmachine Loading… 1.11.6
Add warning for rank_genes_groups
#3792 opened Sep 10, 2025 by grst Loading…
1 of 2 tasks
15
Update zarr requirement from <3 to <4 dependencies Pull requests that update a dependency file python Pull requests that update python code
#3775 opened Aug 25, 2025 by dependabot bot Loading…
Refactor BasePlot: avoid unnecessary DataFrame conversion
#3765 opened Aug 17, 2025 by etching-7z • Draft
3 tasks
feat(plotting): Add group_cmaps parameter to sc.pl.dotplot to specify unique colormaps for each group
#3764 opened Aug 16, 2025 by rwbaber Loading…
1 of 3 tasks
3
performance: Refactor BasePlot & subclasses to copy less
#3757 opened Aug 3, 2025 by dorzhey Loading…
3 tasks done
3
Deprecate save parameter of plots
#3675 opened Jun 7, 2025 by Zethson • Draft
2 of 4 tasks
1.12.0
1
1
(feat): presets
#3653 opened May 28, 2025 by flying-sheep • Draft
1 of 4 tasks
1.12.0
1
1
Remove external tests and deprecate sc.external
#3645 opened May 26, 2025 by flying-sheep • Draft
2 of 3 tasks
1.12.0
1
1
Add neighbors_from_distance for computing neighborhood graphs from precomputed distance matrices
#3627 opened May 8, 2025 by amalia-k510 Loading… 1.12.0
17
Draft PR: Add modularity and modularity_adata functions to scanpy.metrics
#3613 opened Apr 25, 2025 by amalia-k510 Loading… 1.12.0
21
Refactored scanpy.tools._sparse_nanmean to eliminate unnecessary data… benchmark
#3570 opened Apr 8, 2025 by Reovirus Loading…
3 tasks done
1.11.6
1
18
Add cluster_resolution_finder and cluster_decision_tree for help deciding the proper resolution
#3532 opened Mar 28, 2025 by joe-jhou2 Loading…
3 tasks done
1
30
[OWKINxSCVERSE hack]: anndata-plot MVP
#3517 opened Mar 17, 2025 by timtreis • Draft
Faster filtering of sparce matrix
#3465 opened Feb 13, 2025 by kaushalprasadhial Loading…
2 tasks
1
missing var_names in BasePlot
#3460 opened Feb 10, 2025 by FrancescaDr Loading…
1 of 3 tasks
1
2
faster reading of h5ad file (~18X faster)
#3365 opened Nov 14, 2024 by kaushalprasadhial • Draft
3 tasks
1
(feat): seurat v3 with dask Area - Out of core 💾 Working with on disk data Area – Performance 🐌 Area – Preprocessing 🧼
#3340 opened Nov 5, 2024 by ilan-gold • Draft
2 of 3 tasks
1.12.0
1
1
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