Issues

• Possible GRN performance regression in arboreto_with_multiprocessing.py between pySCENIC 0.12.0 and 0.12.1

  aertslab/pySCENIC#640 · Filter by author luyifei111 opened on Sep 28, 2026

• [BUG] pyscenic --help crashes on NumPy >= 1.24: np.object was removed

  bug
  aertslab/pySCENIC#639 · Filter by author baj12 opened on Aug 21, 2026

• some TF in TF gene list is not belong to TF,it's transcrip inhibitors.

  bug
  aertslab/pySCENIC#638 · Filter by author seekning opened on Jun 18, 2026

• [BUG] indexing bug in transform.py causes errors in leading edge computation

  bug
  aertslab/pySCENIC#635 · Filter by author haozhu233 opened on Feb 26, 2026

• ValueError: CisTargetDatabase object is in an inconsistent state: "region_or_gene_ids_loaded" attribute is None, but "df_cached" is not.

  bug
  aertslab/pySCENIC#634 · Filter by author Joyjoyjoyc opened on Feb 11, 2026

• [BUG] aucell pyscenic.cli.pyscenic - ERROR - Expression matrix should be provided in the loom file format.

  bug
  aertslab/pySCENIC#632 · Filter by author HaixJiang opened on Jan 10, 2026

• add binarize function seed

  aertslab/pySCENIC#631 · Filter by author Liripo opened on Nov 20, 2025

• [BUG] src/resources/ contents already provided by ctxcore

  bug
  aertslab/pySCENIC#630 · Filter by author dlaehnemann opened on Nov 14, 2025

• Low regulon recovery in pySCENIC ctx for two butterfly scRNA-seq datasets

  bug
  aertslab/pySCENIC#628 · Filter by author francicco opened on Oct 27, 2025
  1

• Warning message - unsure if process is running or not?

  aertslab/pySCENIC#627 · Filter by author benjytan88 opened on Aug 16, 2025
  1

• [BUG]Running grn but discontinued without any errors

  bug
  aertslab/pySCENIC#626 · Filter by author LynnChan99 opened on Aug 12, 2025
  2

• Low expression and high RSS of regulons

  question
  aertslab/pySCENIC#624 · Filter by author Li-ZhiD opened on Jul 24, 2025

• Significant variation in GRNBoost2 results with minor cell subsampling (removing one cell) in pySCENIC

  aertslab/pySCENIC#623 · Filter by author jklupup opened on Jul 15, 2025
  1

• Attribute errors caused by dependency conflicts in "binarize()"

  aertslab/pySCENIC#622 · Filter by author zhangzihao01 opened on Jun 24, 2025
  2

• [BUG] pyscenic ctx error

  bug
  aertslab/pySCENIC#621 · Filter by author Sophielsn opened on Jun 23, 2025
  2

• Manually Adding ChIP-Seq Data

  aertslab/pySCENIC#619 · Filter by author rayajallad opened on May 28, 2025

• [results] After df2regulons(), gene name formatting in each regulon is weird

  question
  aertslab/pySCENIC#618 · Filter by author redbybeing opened on May 28, 2025
  1

• Issue with the "Intersection of gene_names and tf_names is empty" while running the grnboost2 step of pySCENIC in hpc

  aertslab/pySCENIC#616 · Filter by author npees1 opened on May 24, 2025
  3

• [BUG] Substantially different results when using AUCell vs pyscenic.aucell

  bug
  aertslab/pySCENIC#615 · Filter by author PauBadiaM opened on May 12, 2025

• Batch effet

  aertslab/pySCENIC#614 · Filter by author RunyuXia opened on May 11, 2025

• What do the (+) and (-) represent respectively?

  question
  aertslab/pySCENIC#613 · Filter by author CampingOnSeabed opened on Apr 21, 2025
  1

• [BUG] Output directory is empty

  bug
  aertslab/pySCENIC#611 · Filter by author lzh-fugwaa opened on Apr 2, 2025

• [BUG] My output directory don't have motif enrichment result tsv

  bug
  aertslab/pySCENIC#610 · Filter by author lzh-fugwaa opened on Mar 30, 2025

• [BUG] pyscenic grn errors: Resource temporarily unavailable & empty intersection

  bug
  aertslab/pySCENIC#609 · Filter by author radiasso opened on Mar 18, 2025
  1

• Empty Outputs

  aertslab/pySCENIC#608 · Filter by author rayajallad opened on Mar 7, 2025