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Bug in the sc.pp.scale function when specifying a specific layer

Triage 🩺This issue needs to be triaged by a maintainerThis issue needs to be triaged by a maintainer

Status: Open.

Bug

#3937 In scverse/scanpy;

· scuhkf opened on Jan 7, 2026

Integration Testing CI Test Failure on python 3.13

Status: Open.

#3935 In scverse/scanpy;

· scverse-bot opened on Jan 7, 2026

[RFC] Proposal: Architecture Modernization – Native Kernels, Model Hub & Lazy Dependencies

Area – Performance 🐌

Needs info❔More information neededMore information needed

Status: Open.

Enhancement

#3934 In scverse/scanpy;

· krkawzq opened on Dec 24, 2025

Order of pts and pts_rest in rank_genes_groups results doesn't match other fields in adata.uns["rank_genes_groups"]

Triage 🩺This issue needs to be triaged by a maintainerThis issue needs to be triaged by a maintainer

Status: Open.

Bug

#3930 In scverse/scanpy;

· erlun1 opened on Dec 22, 2025

sc.pl.umap does not show legend when show=False and saving figure manually

Triage 🩺This issue needs to be triaged by a maintainerThis issue needs to be triaged by a maintainer

Status: Open.

Bug

#3926 In scverse/scanpy;

· lihaowhusos opened on Dec 21, 2025

Recommended order for sc.pp.filter_genes and sc.pp.normalize_total in preprocessing pipeline

Triage 🩺This issue needs to be triaged by a maintainerThis issue needs to be triaged by a maintainer

Status: Open.

Enhancement

#3925 In scverse/scanpy;

· baicai-ai opened on Dec 19, 2025

Add TAU as an optional clustering method in Scanpy

Triage 🩺This issue needs to be triaged by a maintainerThis issue needs to be triaged by a maintainer

Status: Open.

Enhancement

#3919 In scverse/scanpy;

· HillelCharbit opened on Dec 15, 2025

Change <code>leiden</code> default <code>flavor</code> to <code>None</code> and warn about impending switch to <code>igraph</code> + warn about speed of <code>igraph</code> being **much** faster

Area – ReproducibilityExact replicationExact replication

dependenciesPull requests that update a dependency filePull requests that update a dependency file

Status: Open.

Enhancement

#3911 In scverse/scanpy;

· ilan-gold opened on Dec 11, 2025

<code>pp.regress_out</code> fails with to many CPU-Cores

Status: Open.

Bug

#3910 In scverse/scanpy;

· Intron7 opened on Dec 11, 2025

·  

1.12.0

Exposing some functions <code>squidpy</code> uses

Area – APIAPI designAPI design

Status: Open.

Enhancement

#3891 In scverse/scanpy;

· selmanozleyen opened on Nov 12, 2025

Highly Variable Genes Selection using CSC <code>dask</code>

Area - Out of core 💾Working with on disk dataWorking with on disk data

Area – Performance 🐌

Status: Open.

Enhancement

#3862 In scverse/scanpy;

· ilan-gold opened on Oct 30, 2025

·  

1.13.0

Implementation of <code>sc.tl.score_genes</code> doesn't match reference

Status: Open.

Bug

#3845 In scverse/scanpy;

· MLubetzki opened on Oct 23, 2025