Skip to content

Issues: scverse/scanpy

Beta
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

493 Open 1,364 Closed
493 Open 1,364 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
Assigned to nobody Loading
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Can we read Xenium data using scanpy? Triage 🩺 This issue needs to be triaged by a maintainer
#3664 opened May 30, 2025 by Yijia-Jiang
sc.get.aggregate with dask Area - Out of core 💾 Working with on disk data Area – Performance 🐌
#3659 opened May 28, 2025 by ilan-gold
Integration Testing CI Test Failure on python 3.12
#3651 opened May 28, 2025 by scverse-bot
1
1
generalize sc.tl.embedding_density() to use any 'obsm' key Triage 🩺 This issue needs to be triaged by a maintainer
#3642 opened May 21, 2025 by fishjo
sc.pp.scale dask differs from csr sparse
#3633 opened May 17, 2025 by scverse-bot 1.12.0
@flying-sheep @ilan-gold
3
Dask QC-doesn't work Area - Out of core 💾 Working with on disk data
#3632 opened May 16, 2025 by Intron7
3 tasks done
@ilan-gold
read_10x_mtx() cannot handle numerical barcodes properly (BD Rhapsody specifically) Triage 🩺 This issue needs to be triaged by a maintainer
#3624 opened May 7, 2025 by pormr
2 of 3 tasks
1
scanpy plot Needs info❔ More information needed
#3617 opened May 1, 2025 by WeihangChen0
2 of 3 tasks
1
Add Seurat compatibility flavor Area – API API design Meta A meta-request to be implemented in multiple steps
#3609 opened Apr 24, 2025 by flying-sheep
4 tasks
@flying-sheep @ilan-gold
AnnData' object has no attribute '_obsm
#3602 opened Apr 19, 2025 by HDEzhsw
2 of 3 tasks
1
sc.read_10x_mtx KeyError: 2 The above exception was the direct cause of the following exception: Needs info❔ More information needed
#3601 opened Apr 18, 2025 by Advancer123
3 tasks done
1
Default legend when scaling dotplots Triage 🩺 This issue needs to be triaged by a maintainer
#3576 opened Apr 11, 2025 by EliasFarr
Scanpy’s tests should prevent DeprecationWarnings and FutureWarnings Development Process 🚀
#3558 opened Apr 4, 2025 by flying-sheep 1.11.3
@flying-sheep
Whether the highly variable gene selection method seurat_v3 of Scanpy is really the same as the vst method of Seurat.
#3542 opened Mar 30, 2025 by AdotaLover
2 of 3 tasks
2
Enhance Clustering Resolution Selection with Hierarchical Tree Visualization Area - Plotting 🌺
#3533 opened Mar 28, 2025 by joe-jhou2
1
2
segmentation fault (SIGSEGV) when computing neighbors Needs info❔ More information needed
#3507 opened Mar 14, 2025 by Hrovatin
2 of 3 tasks
6
[Question]: Usage of Graph Algorithms and Any Slowdowns?
#3476 opened Feb 20, 2025 by nv-rliu
3
Add support for backed mode in calculate_qc_metrics
#3464 opened Feb 12, 2025 by milos7250
2
feature selection method using pearson residuals discrepancies Question
#3452 opened Jan 24, 2025 by jflucier
2 of 3 tasks
1.12.0
3
UMAP redesign Area - Topology 🍩 Neighbor graphs Area – API API design Meta A meta-request to be implemented in multiple steps
#3429 opened Jan 9, 2025 by flying-sheep
UMAP implementation in igraph
#3408 opened Dec 18, 2024 by iosonofabio
@ricor07
3
Allow both 'on data' legend together with legend on righ-hand side of plot Area - Plotting 🌺 Area – API API design
#3401 opened Dec 13, 2024 by mumichae
1
"Interactive" Dotplot version: check for available var_names Area - Plotting 🌺
#3387 opened Nov 25, 2024 by FrancescaDr
1
1
Difference between tl.rank_genes_groups and pl.rank_genes_groups_heatmap
#3378 opened Nov 20, 2024 by LioLenr
Nan values after running sc.tl.filter_rank_genes_groups and plotting
#3374 opened Nov 18, 2024 by shreyii
1
ProTip! Follow long discussions with comments:>50.