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The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81

Status: Open.

#629 In aertslab/scenicplus;

· danli349 opened on Feb 25, 2026

How to interpret scenic plus results

Status: Open.

#628 In aertslab/scenicplus;

· niconps14 opened on Feb 16, 2026

Small change in dataset yields large change in results

Status: Open.

#627 In aertslab/scenicplus;

· sarah-chapin opened on Feb 10, 2026

ValueError: Shape of passed values is (8633, 1), indices imply (4451, 1)

Status: Open.

#626 In aertslab/scenicplus;

· danli349 opened on Feb 6, 2026

Query about strategy in running scenicplus

Status: Open.

#623 In aertslab/scenicplus;

· malonzm1 opened on Jan 30, 2026

Disappearing transciption factor

Status: Open.

#622 In aertslab/scenicplus;

· malonzm1 opened on Jan 28, 2026

ValueError: Fragment file ./tmp/TCEV_Multiome1/DediffT_C345.fragments.tsv.gz does not exist.

Status: Open.

#621 In aertslab/scenicplus;

· danli349 opened on Jan 7, 2026

How can I build the <code>scenicplus_development_tutorial</code> conda envirement?

Status: Open.

#619 In aertslab/scenicplus;

· danli349 opened on Dec 17, 2025

Running scenicplus without internet connection

Status: Open.

#618 In aertslab/scenicplus;

· malonzm1 opened on Dec 17, 2025

<code>pycistopic</code> UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools&lt;81.

Status: Open.

#617 In aertslab/scenicplus;

· danli349 opened on Dec 16, 2025

heatmap_dotplot / generate_dotplot_df misalign cell annotations when mod.to_df() returns rows in a different order (groupby uses wrong labels)

Status: Open.

#614 In aertslab/scenicplus;

· kahoitoh opened on Dec 9, 2025

MissingOutputException in rule download_genome_annotations

Status: Open.

#611 In aertslab/scenicplus;

· biocclh opened on Nov 17, 2025