Issues

• Integration Testing CI Test Failure on python 3.13

  scverse/SnapATAC2#513 · Filter by author scverse-issue-creator opened on Oct 21, 2026

• Unable to subset cells from backed anndata object after preprocessing

  scverse/SnapATAC2#512 · Filter by author PierreFumeron opened on Oct 19, 2026

• Integration Testing CI Test Failure on python 3.14

  scverse/SnapATAC2#511 · Filter by author scverse-issue-creator opened on Oct 18, 2026

• Integration Testing CI Install Failure on python 3.12

  scverse/SnapATAC2#510 · Filter by author scverse-issue-creator opened on Oct 15, 2026

• Integration Testing CI Test Failure on python 3.12

  scverse/SnapATAC2#509 · Filter by author scverse-issue-creator opened on Oct 11, 2026

• Make igraph optional

  scverse/SnapATAC2#505 · Filter by author Zethson opened on Sep 28, 2026
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• Integration Testing CI Install Failure on python 3.14 with prerelease dependencies

  scverse/SnapATAC2#491 · Filter by author scverse-issue-creator opened on Aug 5, 2026

• Integration Testing CI Install Failure on python 3.14

  scverse/SnapATAC2#489 · Filter by author scverse-issue-creator opened on Aug 5, 2026

• Integration Testing CI Test Failure on python 3.14 with prerelease dependencies

  scverse/SnapATAC2#466 · Filter by author scverse-issue-creator opened on Jun 3, 2026

• make_fragment_file silently drops marked duplicates, making frac_duplicates always 0 and fragment counts always 1

  scverse/SnapATAC2#464 · Filter by author anagchar opened on May 18, 2026
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• Issue with empty UMAP Plot in SnapATAC2 (v2.9.0)

  scverse/SnapATAC2#456 · Filter by author yellowlemon8 opened on Apr 2, 2026

• Feature Request/Support: Support for mixed fragment_single and fragment_paired keys in AnnDataSet

  scverse/SnapATAC2#452 · Filter by author wkl1990 opened on Mar 12, 2026

• Integration Testing CI Install Failure on python 3.13

  scverse/SnapATAC2#451 · Filter by author scverse-issue-creator opened on Mar 12, 2026

• Integrating Charton for publication-quality, Rust-native plotting (Polars-compatible)

  scverse/SnapATAC2#450 · Filter by author wangjiawen2013 opened on Mar 1, 2026

• Integration Testing CI Test Failure on python 3.13 with prerelease dependencies

  scverse/SnapATAC2#448 · Filter by author scverse-bot opened on Jan 31, 2026

• scvi.external.POISSONMULTIVI function error

  scverse/SnapATAC2#433 · Filter by author tianlt opened on Nov 11, 2025
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• Empty peak matrix

  scverse/SnapATAC2#422 · Filter by author KyriakisDimitrios opened on Oct 15, 2025

• Plotting issue on fresh install

  scverse/SnapATAC2#420 · Filter by author f6v opened on Oct 7, 2025
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• unable to install a functioning app on a fresh environment

  scverse/SnapATAC2#409 · Filter by author zelhar opened on Aug 1, 2025
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• multiple sample version of Annotating cell clusters by integrating single-cell RNA-seq data

  scverse/SnapATAC2#406 · Filter by author Cmfffff opened on Jul 18, 2025
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• Question about integrating unpaired data

  scverse/SnapATAC2#402 · Filter by author huziouziou opened on Jun 22, 2025

• ex.export_coverage fails with some probloms

  scverse/SnapATAC2#398 · Filter by author RaFenglei opened on May 23, 2025

• custom reference genome and annotation support

  scverse/SnapATAC2#394 · Filter by author sbgonenc opened on May 2, 2025
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• Using SCENIC+ with clustered and annotated anndataset

  scverse/SnapATAC2#393 · Filter by author ananyakohli17 opened on Apr 3, 2025

• Is that possible to run diff_test in parallel?

  scverse/SnapATAC2#392 · Filter by author beyondpie opened on Apr 2, 2025
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