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513 Open 1,253 Closed
513 Open 1,253 Closed
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Issues list

Difference between tl.rank_genes_groups and pl.rank_genes_groups_heatmap
#3378 opened Nov 20, 2024 by LioLenr
Rank genes groups wilcoxon test fails for more than 10 million cells Bug 🐛 Triage 🩺 This issue needs to be triaged by a maintainer
#3377 opened Nov 19, 2024 by abs51295
3 tasks done
Nan values after running sc.tl.filter_rank_genes_groups and plotting
#3374 opened Nov 18, 2024 by shreyii
Switch to numpy.random.Generator Area – Reproducibility Exact replication Enhancement ✨
#3371 opened Nov 18, 2024 by flying-sheep
Error in Scanpy Doublet Analysis with Scrublet on .h5ad Data Using backed="r+" Bug 🐛 Triage 🩺 This issue needs to be triaged by a maintainer
#3370 opened Nov 15, 2024 by simang5c
2 of 3 tasks
Add mask to sc.pp.subsample Area – Preprocessing 🧼 Enhancement ✨
#3368 opened Nov 14, 2024 by flying-sheep 1.11.0
@flying-sheep
sc.pl.heatmap var_names function KeyError Bug 🐛 Triage 🩺 This issue needs to be triaged by a maintainer
#3363 opened Nov 13, 2024 by josenimo
3 tasks done
Fix “preprocessing” docs page Area - Documentation 📒 Bug 🐛
#3360 opened Nov 12, 2024 by flying-sheep
I started using scanny to read in data, but I always got the following error. I can't find any other detailed reasons.
#3355 opened Nov 12, 2024 by xzt199610
Implementation of fireducks pandas Enhancement ✨ Triage 🩺 This issue needs to be triaged by a maintainer
#3348 opened Nov 11, 2024 by KarlKaise
Dask docs Area - Documentation 📒 Area - Out of core 💾 Working with on disk data Enhancement ✨
#3346 opened Nov 8, 2024 by flying-sheep
@Intron7 @ilan-gold @mikelkou
scanpy installation on colab without any GPU's Bug 🐛 Triage 🩺 This issue needs to be triaged by a maintainer
#3345 opened Nov 8, 2024 by CRISTIANJULIOCESAR
1 of 3 tasks
3
Cannot read Visium HD data using spatialdata-io (Recurrent error). Data is non-zarr format. Bug 🐛 Triage 🩺 This issue needs to be triaged by a maintainer
#3342 opened Nov 6, 2024 by ankshe91
2 of 3 tasks
11
Issues with reading in non zarr format Visium HD data in python Bug 🐛 Triage 🩺 This issue needs to be triaged by a maintainer
#3341 opened Nov 5, 2024 by ankshe
2 of 3 tasks
Documentation typo for scanpy.pp.filter_cells
#3332 opened Oct 30, 2024 by fionaEyoung
ValueError: Output dtype not compatible with inputs. Bug 🐛 Triage 🩺 This issue needs to be triaged by a maintainer
#3331 opened Oct 30, 2024 by ianfd
2 of 3 tasks
1
Feature Request: Option to Plot Highest Absolute Values on Top in sc.pl.umap Area - Plotting 🌺 Enhancement ✨
#3326 opened Oct 25, 2024 by tobias-zehnder
scanpy.pl.stacked_violin - remove "marker label" whitespace if var_names is a list of genes Area - Plotting 🌺 Bug 🐛
#3320 opened Oct 24, 2024 by adkinsrs
3 tasks done
6
Multibatchnorm / between library batch normalization Enhancement ✨ Triage 🩺 This issue needs to be triaged by a maintainer
#3309 opened Oct 23, 2024 by Marwansha
negative values after score_genes with log1P or counts layer
#3297 opened Oct 20, 2024 by Li-ZhiD
Gearys C and Morans I As Public API Enhancement ✨
#3291 opened Oct 17, 2024 by ilan-gold
@Intron7
Plotting colors from obsm Enhancement ✨ Triage 🩺 This issue needs to be triaged by a maintainer
#3277 opened Oct 10, 2024 by canergen
ScanPy's BSD license and GPLed dependencies Question
#3272 opened Oct 1, 2024 by PertuyF
1
sc.tl.score_genes -- ValueError: No valid genes were passed for scoring Bug 🐛 Triage 🩺 This issue needs to be triaged by a maintainer
#3266 opened Sep 26, 2024 by xyang2uchicago
3 tasks done
AttributeError: Can only use .str accessor with string values! Bug 🐛 Needs info❔ More information needed
#3261 opened Sep 26, 2024 by DUAN-GAO
2 of 3 tasks
3
ProTip! What’s not been updated in a month: updated:<2024-10-21.