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Pull requests: scverse/scanpy

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72 Open 1,706 Closed
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Pull requests list

[pre-commit.ci] pre-commit autoupdate
#3688 opened Jun 16, 2025 by pre-commit-ci bot Loading…
1
Update numpy array comparisons to use isin
#3685 opened Jun 13, 2025 by emmanuel-ferdman Loading…
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
1.11.3
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
~ 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
fix bug for partial_fit when the number of batch samples is less than n_comp
#3313 opened Oct 23, 2024 by DingWB Loading…
2 of 3 tasks
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
t-SNE optimization using scikit-learn-intelex
#3279 opened Oct 11, 2024 by kaushalprasadhial Loading…
2
Add sanitize to score_genes
#3262 opened Sep 26, 2024 by flying-sheep • Draft
3 tasks
1
Less hacky plotting classes
#3209 opened Aug 13, 2024 by flying-sheep • Draft
9
Switch dendrogram implementation to aggregate
#3204 opened Aug 9, 2024 by flying-sheep • Draft
2 of 3 tasks
1
1
add layer argument for sc.tl.score_genes_cell_cycle
#3138 opened Jul 2, 2024 by shinthor • Draft
1 of 3 tasks
1.12.0
2
Update ingest example. Fixes AttributeError: 'Ingest' object has no attribute '_pca_use_hvg'
#3075 opened May 22, 2024 by siebrenf Loading…
3 tasks done
1
2
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