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Mislocation of colorbar legend by <code>sc.pl.scatter</code>

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

Status: Open.

Bug

#3963 In scverse/scanpy;

· Fantasque68 opened on Jan 30, 2026

Transposing error with sce.pp.harmony_integrate()

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

Status: Open.

Bug

#3962 In scverse/scanpy;

· hannahwilcox1011 opened on Jan 29, 2026

Plotting UMAP converts cell_id to category --&gt; hinders plotting with spatialdata.plot

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

Status: Open.

Bug

#3960 In scverse/scanpy;

· KarolineHoller opened on Jan 29, 2026

Add Poisson Gene Selection to HVG

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

Status: Open.

Enhancement

#3956 In scverse/scanpy;

· Intron7 opened on Jan 26, 2026

[Bug] Kernel crash using harmony

Needs info❔More information neededMore information needed

Status: Open.

Bug

#3946 In scverse/scanpy;

· SunYong0821 opened on Jan 16, 2026

[RFC] Refactoring Scanpy's Numba Backend: C-Style Kernel Layer &amp; Biology-Optimized Sparse Matrices

Status: Open.

Enhancement

#3944 In scverse/scanpy;

· krkawzq opened on Jan 12, 2026

<code>scanpy.external.pp.harmony_integrate</code> incompatible with newly updated <code>harmonypy&gt;=0.1.0</code>

Area – ExternalDealing with external toolsDealing with external tools

Status: Open.

Enhancement

#3940 In scverse/scanpy;

· kiklata opened on Jan 12, 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 &amp; 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