scverse / scanpy Public

Notifications
Fork 614
Star 2k

Code
Issues 497
Pull requests 73
Actions
Projects 1
Security
Insights

Additional navigation options

Code
Issues
Pull requests
Actions
Projects
Security
Insights

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.

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

497 Open 1,322 Closed

Author

Filter by author

Label

Filter by label

Use alt + click/return to exclude labels

or ⇧ + click/return for logical OR

Projects

Filter by project

Milestones

Filter by milestone

Assignee

Filter by who’s assigned

Assigned to nobody

Sort

Sort by

Newest Oldest Most commented Least commented Recently updated Least recently updated Best match

Most reactions

Issues list

Why the deleted gene is still in the sc.tl.rank_genes_groups output? Triage 🩺

This issue needs to be triaged by a maintainer

#3513 opened Mar 14, 2025 by danli349

1 of 3 tasks

Boxplots without violin plot? Triage 🩺

This issue needs to be triaged by a maintainer

#3512 opened Mar 14, 2025 by ivykos

segmentation fault (SIGSEGV) when computing neighbors Triage 🩺

This issue needs to be triaged by a maintainer

#3507 opened Mar 14, 2025 by Hrovatin

2 of 3 tasks

Add Baumgartner-Weiss-Schindler test to sc.tl.rank_genes_groups()

#3503 opened Mar 11, 2025 by JakeLehle

dask sparse PCA dtype Triage 🩺

This issue needs to be triaged by a maintainer

#3487 opened Feb 26, 2025 by ilan-gold

3 tasks done

[Question]: Usage of Graph Algorithms and Any Slowdowns?

#3476 opened Feb 20, 2025 by nv-rliu

'ingest' on scvi-batch corrected reference? Needs info❔

More information needed

#3469 opened Feb 17, 2025 by ShuonanChen

Scanpy doesn't identify markers in marker genes dict but does as a string Triage 🩺

This issue needs to be triaged by a maintainer

#3468 opened Feb 17, 2025 by jcshuy

1 of 3 tasks

converting strings to categoricals Area - IO

Reading and writing

Area – API

API design

#3467 opened Feb 17, 2025 by wangjiawen2013 1.12.0

Add support for backed mode in calculate_qc_metrics

#3464 opened Feb 12, 2025 by milos7250

Plot violin throws error when trying to change density argument

#3458 opened Feb 5, 2025 by LinearParadox

3 tasks done

feature selection method using pearson residuals discrepancies Question

#3452 opened Jan 24, 2025 by jflucier

2 of 3 tasks

1.12.0

fast array utils spinoff package Area – API

API design

Meta

A meta-request to be implemented in multiple steps

#3429 opened Jan 9, 2025 by flying-sheep

Support for scipy.csr_array/scipy.csc_array

#3423 opened Jan 1, 2025 by alam-shahul

2 of 3 tasks

1.12.0

UMAP implementation in igraph

#3408 opened Dec 18, 2024 by iosonofabio

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

mask_obs parameter modifies obs column when calling scatterplot Area - Plotting 🌺

#3400 opened Dec 13, 2024 by mumichae

3 tasks done

"Interactive" Dotplot version: check for available var_names Area - Plotting 🌺

#3387 opened Nov 25, 2024 by FrancescaDr

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

Switch to numpy.random.Generator Area – Reproducibility

Exact replication

Provide feedback

Saved searches

Use saved searches to filter your results more quickly