Skip to content

Issues: scverse/scanpy

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

510 Open 1,252 Closed
510 Open 1,252 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

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
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
Add scran nomalisation into scanpy Area – Preprocessing 🧼 Enhancement ✨
#3255 opened Sep 23, 2024 by le-ander
2
io submodule from anndata Enhancement ✨
#3245 opened Sep 20, 2024 by ilan-gold
1 of 3 tasks
Why making feature names unique instead of aggregation? Enhancement ✨ Question
#3241 opened Sep 18, 2024 by VladimirShitov
6
pbmc68k_reduced raw counts
#3224 opened Sep 4, 2024 by MartaBenegas
ProTip! Updated in the last three days: updated:>2024-11-13.