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Integration Testing CI Test Failure on python 3.14

Status: Open.

#198 In scverse/muon;

· scverse-issue-creator opened on May 25, 2026

Integration Testing CI Test Failure on python 3.12

Status: Open.

#197 In scverse/muon;

· scverse-issue-creator opened on May 25, 2026

[Feature Request] MACS3 support as optional peak caller alongside MACS2

enhancementNew feature or requestNew feature or request

Status: Open.

#196 In scverse/muon;

· BDBGenomics opened on May 22, 2026

[Enhancement] Add bulk ATAC-seq AnnData ingestion path to the atac module

Status: Open.

#195 In scverse/muon;

· BDBGenomics opened on May 22, 2026

[Bug] count_fragments_features ignores strand orientation for extend_upstream/extend_downstrea

bugSomething isn't workingSomething isn't working

Status: Open.

#194 In scverse/muon;

· BDBGenomics opened on May 22, 2026

Integration Testing CI Test Failure on python 3.14 with prerelease dependencies

Status: Open.

#190 In scverse/muon;

· scverse-issue-creator opened on May 9, 2026

mu.pl.embedding layers substitues the content of mudata.X

bugSomething isn't workingSomething isn't working

Status: Open.

#183 In scverse/muon;

· dawe opened on Apr 1, 2026

Having .raw objects in the constituent modalities can cause incorrect embedding plots when var_names are different

bugSomething isn't workingSomething isn't working

Status: Open.

#162 In scverse/muon;

· timslittle opened on Jun 27, 2025

Add single cell HiC datasets into Muon container

Status: Open.

#159 In scverse/muon;

· Xuyuch opened on Mar 12, 2025

Parse modality prefix for gene IDs

enhancementNew feature or requestNew feature or request

Status: Open.

#156 In scverse/muon;

· gtca opened on Feb 10, 2025

random_state=0 does not set seed in muon.tl.leiden, either a bug or unclear documentation

bugSomething isn't workingSomething isn't working

Status: Open.

#154 In scverse/muon;

· AKMHamid opened on Dec 12, 2024

Document how to make a release

enhancementNew feature or requestNew feature or request

Status: Open.

#153 In scverse/muon;

· grst opened on Dec 10, 2024