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Issues list

Fix link to preprocessing recipe link in trajectory inference tutorial Area - Documentation 📒

#3584 opened Apr 11, 2025 by swstkm

3 tasks done

_create_adata in test_score_genes doesen't work properly Triage 🩺

This issue needs to be triaged by a maintainer

#3580 opened Apr 11, 2025 by Reovirus

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 1.11.2

Investigate annoy out-of-core Area - Out of core 💾

Working with on disk data

#3557 opened Apr 3, 2025 by flying-sheep 1.12.0

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

Enhance Clustering Resolution Selection with Hierarchical Tree Visualization Area - Plotting 🌺

#3533 opened Mar 28, 2025 by joe-jhou2

segmentation fault (SIGSEGV) when computing neighbors

#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

[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

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

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