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Batch Key not working with sc.pp.scrublet()

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

Status: Open.

Bug

#3837 In scverse/scanpy;

· zekepuli opened on Oct 17, 2025

spaceranger’s automated cluster number detection

Needs info❔More information neededMore information needed

Status: Open.

Enhancement

#3834 In scverse/scanpy;

· asmlgkj opened on Oct 14, 2025

Add <code>jaccard</code> as an additional <code>method</code> in <code>sc.pp.neighbors</code>

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

Status: Open.

Enhancement

#3828 In scverse/scanpy;

· jpintar opened on Oct 5, 2025

Export more types

Area – APIAPI designAPI design

Status: Open.

Enhancement

#3826 In scverse/scanpy;

· flying-sheep opened on Oct 2, 2025

Apple Silicon: Accelerate or openBLAS for Numpy

Question

Status: Open.

Enhancement

#3823 In scverse/scanpy;

· mxp0wr opened on Sep 30, 2025

Output numer of observations aggregated from <code>scanpy.get.aggregate</code>

Area – APIAPI designAPI design

Area – Differential ExpressionDifferential expressionDifferential expression

good first issueeasy first issue to get started in OSS community contribution!easy first issue to get started in OSS community contribution!

Status: Open.

Enhancement

#3822 In scverse/scanpy;

· ilan-gold opened on Sep 30, 2025

Unexpected number of non-zero distances when running <code>sc.pp.neighbors</code> with <code>transformer="pynndescent"</code>

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

Status: Open.

Bug

#3809 In scverse/scanpy;

· jpintar opened on Sep 21, 2025

Custom neighbor transformers with variable neighbor count &lt;= k fail

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

Status: Open.

Bug

#3806 In scverse/scanpy;

· maltekuehl opened on Sep 19, 2025

sc.tl.paga ValueError: mismatching number of index arrays for shape; got 0, expected 2

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

Status: Open.

Bug

#3805 In scverse/scanpy;

· eroell opened on Sep 19, 2025

Inconsistency of <code>basis</code> argument in plotting functions

Area - Plotting 🌺

Status: Open.

Bug

#3803 In scverse/scanpy;

· lazappi opened on Sep 18, 2025

Integration Testing CI Test Failure on python 3.11

Status: Open.

#3791 In scverse/scanpy;

· scverse-bot opened on Sep 10, 2025

tests for sc.pl.diffmap and sc.pl.rank_genes_groups

Area - Plotting 🌺

Status: Open.

Enhancement

#3787 In scverse/scanpy;

· sueoglu opened on Sep 5, 2025