scverse/SnapATAC2

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Single-cell epigenomics analysis tools

Stars: 323
Forks: 43
Open beginner issues: 0
Indexed issues: 68

Dominant language: Python
License: MIT
Last GitHub push: Aug 14, 2026
Latest indexed: Sep 19, 2026
Contributing guide: No contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

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68 open issues indexed

Integration Testing CI Test Failure on python 3.12 Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/SnapATAC2#501 · Opened Sep 16, 2026
Integration Testing CI Test Failure on python 3.14 Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/SnapATAC2#500 · Opened Sep 14, 2026
Integration Testing CI Install Failure on python 3.14 with prerelease dependencies Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

scverse/SnapATAC2#491 · Opened Aug 5, 2026
Integration Testing CI Install Failure on python 3.12 Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

scverse/SnapATAC2#490 · Opened Aug 5, 2026
Integration Testing CI Install Failure on python 3.14 Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/SnapATAC2#489 · Opened Aug 5, 2026
Integration Testing CI Test Failure on python 3.14 with prerelease dependencies Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/SnapATAC2#466 · Opened Jun 3, 2026
make_fragment_file silently drops marked duplicates, making frac_duplicates always 0 and fragment counts always 1 Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

scverse/SnapATAC2#464 · 1 comment · Opened May 18, 2026
Issue with empty UMAP Plot in SnapATAC2 (v2.9.0) Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/SnapATAC2#456 · Opened Apr 2, 2026
Feature Request/Support: Support for mixed fragment_single and fragment_paired keys in AnnDataSet Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/SnapATAC2#452 · Opened Mar 12, 2026
Integration Testing CI Install Failure on python 3.13 Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/SnapATAC2#451 · Opened Mar 12, 2026
Integrating Charton for publication-quality, Rust-native plotting (Polars-compatible) Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/SnapATAC2#450 · Opened Mar 1, 2026
Integration Testing CI Test Failure on python 3.13 with prerelease dependencies Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

scverse/SnapATAC2#448 · Opened Jan 31, 2026
scvi.external.POISSONMULTIVI function error Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

scverse/SnapATAC2#433 · 1 comment · Opened Nov 11, 2025
Empty peak matrix Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/SnapATAC2#422 · Opened Oct 15, 2025
Plotting issue on fresh install Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

scverse/SnapATAC2#420 · 1 comment · Opened Oct 7, 2025
unable to install a functioning app on a fresh environment Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/SnapATAC2#409 · 1 comment · Opened Aug 1, 2025
multiple sample version of Annotating cell clusters by integrating single-cell RNA-seq data Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

scverse/SnapATAC2#406 · 1 comment · Opened Jul 18, 2025
Question about integrating unpaired data Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/SnapATAC2#402 · Opened Jun 22, 2025
ex.export_coverage fails with some probloms Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/SnapATAC2#398 · Opened May 23, 2025
custom reference genome and annotation support Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/SnapATAC2#394 · 1 comment · Opened May 2, 2025
Using SCENIC+ with clustered and annotated anndataset Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

scverse/SnapATAC2#393 · Opened Apr 3, 2025
Is that possible to run diff_test in parallel? Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/SnapATAC2#392 · 1 comment · 1 reaction · Opened Apr 2, 2025
Macs3 runs out of memory due to multiprocessing when run from a python script. Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

scverse/SnapATAC2#390 · Opened Mar 18, 2025
Memory allocation error (?) when running snap.pp.import_data Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

scverse/SnapATAC2#389 · 2 comments · Opened Mar 17, 2025
guarddog detected repository_integrity_mismatch Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/SnapATAC2#388 · Opened Mar 17, 2025
Nan error in RNA-ATAC integration Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

scverse/SnapATAC2#381 · 1 comment · Opened Feb 27, 2025
Making AnnDataSet changes reflect in individual sample files Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/SnapATAC2#376 · 3 comments · Opened Jan 31, 2025
Bug running harmony batch correction with multiple covariates Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/SnapATAC2#370 · 1 comment · Opened Dec 13, 2024
Unable to edit backed AnnData Open

enhancement :sparkles:

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/SnapATAC2#369 · 2 comments · Opened Dec 11, 2024
The value of 'Fraction of high-quality fragments overlapping peaks' is greater than 1 Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

scverse/SnapATAC2#362 · Opened Nov 18, 2024
Cannot compute joint embedding on RNA and ATAC object Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

scverse/SnapATAC2#350 · 4 comments · Opened Oct 9, 2024
Is there a way generate a coverage plot for DARs? Open

enhancement :sparkles:

Difficulty 5/5 Over a week Newbie friendliness 20/100

scverse/SnapATAC2#337 · 2 comments · Opened Sep 6, 2024
snap.tl.macs3 error Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

scverse/SnapATAC2#336 · 5 comments · Opened Sep 5, 2024
macs3 function not works with multiple dataset Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/SnapATAC2#332 · 4 comments · Opened Sep 2, 2024
AnnDataSet can not be converted to AnnData when the X is empty Open

bug :bug:

Difficulty 3/5 1-2 days Newbie friendliness 42/100

scverse/SnapATAC2#331 · 3 comments · Opened Aug 30, 2024
Label Transfer Using the SCVI-tools Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

scverse/SnapATAC2#326 · 1 comment · Opened Aug 23, 2024
Downstream analysis tutorial Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

scverse/SnapATAC2#319 · 2 comments · Opened Aug 4, 2024
Extracting fragment count matrix Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

scverse/SnapATAC2#316 · 5 comments · Opened Jul 18, 2024
Vignette for downstream analysis tools? Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/SnapATAC2#315 · 4 comments · 3 reactions · Opened Jul 16, 2024
Unexpected behavior in AnnDataSet subset Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/SnapATAC2#310 · 3 reactions · Opened Jun 24, 2024
snapatac2.tl.diff_test Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

scverse/SnapATAC2#306 · 2 comments · Opened May 22, 2024
Accessing and plotting QC metrics after merging to AnnDataSet: more documentation needed Open

documentation :book:

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/SnapATAC2#300 · 2 comments · Opened Apr 26, 2024
Error related to parallelism when running `snap.tl.macs3` when running on the cluster Open

documentation :book:

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

scverse/SnapATAC2#298 · 2 comments · 1 reaction · Opened Apr 22, 2024
hard to understand about the description in filter features. Open

Difficulty 1/5 Under an hour Newbie friendliness 35/100

scverse/SnapATAC2#290 · 1 comment · Opened Apr 8, 2024
add_cor_scores Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

scverse/SnapATAC2#286 · 4 comments · Opened Apr 2, 2024
obs_names resets to original barcodes when assigned via AnnDataset Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/SnapATAC2#278 · Opened Mar 30, 2024
trouble with pbmc notebook Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

scverse/SnapATAC2#277 · 4 comments · Opened Mar 28, 2024
SnapATAC2 Docker Image Pushed to Docker Hub Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

scverse/SnapATAC2#263 · Opened Mar 16, 2024
add_cor_scores could only selects capitalized genes? Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/SnapATAC2#260 · 1 comment · Opened Mar 15, 2024
Read bam with split reads Open

enhancement :sparkles:

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/SnapATAC2#259 · 5 comments · Opened Mar 14, 2024

scverse/SnapATAC2

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