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Pull requests: scverse/scanpy

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Pull requests list

fix: add compat with pandas 3
#3929 opened Dec 22, 2025 by flying-sheep Loading…
1 of 5 tasks
1.12.0
2
Now printing to log.debug (vs warning) when a file name comprises multiple dots (closes #3899)
#3924 opened Dec 18, 2025 by nicolasrochette Loading…
1 of 3 tasks
1
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…
1
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 • Draft
2 of 3 tasks
2
1
Refactor BasePlot: avoid unnecessary DataFrame conversion
#3765 opened Aug 17, 2025 by etching-7z • Draft
3 tasks
feat(plotting): Add group_colors parameter to sc.pl.dotplot to specify unique, perceptually uniform colormaps for each group
#3764 opened Aug 16, 2025 by rwbaber Loading…
1 of 3 tasks
6
performance: Refactor BasePlot & subclasses to copy less
#3757 opened Aug 3, 2025 by dorzhey Loading…
3 tasks done
3
(feat): presets
#3653 opened May 28, 2025 by flying-sheep • Draft
1 of 4 tasks
1.13.0
1
2
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
feat: add modularity and modularity_adata to scanpy.metrics
#3613 opened Apr 25, 2025 by amalia-k510 Loading… 1.12.0
1
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
21
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
~ 35.63% faster filtering
#3330 opened Oct 29, 2024 by kaushalprasadhial • Draft
3 tasks
2
Benchmark dask benchmark
#3319 opened Oct 24, 2024 by mikelkou Loading…
1
@mikelkou
2
lets umap run in parallel
#3295 opened Oct 18, 2024 by Intron7 Loading…
1
21
scale function(_get_mean_var) updated for dense array, speedup upto ~4.65x
#3280 opened Oct 11, 2024 by kaushalprasadhial Loading…
@Intron7 @mikelkou
13
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