Issues

• Bug report [BUG] create_cistopic_object fails with InvalidIndexError whenever min cell != 1

  aertslab/pycisTopic#230 · Filter by author dmuratli opened on Jul 15, 2026

• [Bug] get_tss_annotation_from_ensembl produces pyarrow.lib.ArrowTypeError when chromosome column contains mixed types

  aertslab/pycisTopic#229 · Filter by author BDBGenomics opened on May 22, 2026
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• ValueError: Unable to determine Axes to steal space for Colorbar. Either provide the *cax* argument to use as the Axes for the Colorbar, provide the *ax* argument to steal space from it, or add *mappable* to an Axes.

  aertslab/pycisTopic#224 · Filter by author danli349 opened on Feb 11, 2026

• PanicException: called Result::unwrap() on an Err value: ParseIntError { kind: InvalidDigit }

  aertslab/pycisTopic#221 · Filter by author danli349 opened on Dec 23, 2025
  1

• pycistopic pyarrow.lib.ArrowTypeError: Expected bytes, got a 'int' object

  aertslab/pycisTopic#219 · Filter by author danli349 opened on Dec 17, 2025
  1

• Bug report [BUG] export_pseudobulk using new cellranger-arc v2.1 fragment files

  aertslab/pycisTopic#217 · Filter by author mariefbourdon opened on Dec 12, 2025
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• Bug report [BUG] Tutorial throws pyarrow.lib.ArrowTypeError: Expected bytes, got a 'int' object

  aertslab/pycisTopic#215 · Filter by author arne-cl opened on Sep 19, 2025
  3

• Bug report [BUG]: Unable to export region accessibility to loom TypeError: Object dtype dtype('O') has no native HDF5 equivalent

  aertslab/pycisTopic#214 · Filter by author jjia1 opened on Sep 12, 2025
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• Bug Report: OutOfMemoryError (“GC overhead limit exceeded”) when running topic modeling with Mallet

  aertslab/pycisTopic#213 · Filter by author teng-gao opened on Jul 25, 2025
  3

• Guidance on V3 branch

  aertslab/pycisTopic#212 · Filter by author jjia1 opened on Jul 24, 2025
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• Bug report [BUG] - pycisTopic QC

  aertslab/pycisTopic#210 · Filter by author TheeJonas opened on Jun 19, 2025
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• KeyError in cell_topic_heatmap [BUG]

  aertslab/pycisTopic#209 · Filter by author daniel-nebdal opened on May 26, 2025
  1

• Error in topic binarization after topic modeling with polars_1xx branch

  aertslab/pycisTopic#206 · Filter by author Sebdumas opened on Mar 17, 2025
  2

• High Memory Consumption During QC Process

  aertslab/pycisTopic#198 · Filter by author Keep-Raining opened on Dec 31, 2024
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• Problem installing polars_1xx branch, possible issue through pybigtools [BUG]

  aertslab/pycisTopic#197 · Filter by author ckv2115147 opened on Dec 30, 2024
  2

• pycisTopic find_diff_features function stopping abruptly at Starting a local Ray instance

  aertslab/pycisTopic#195 · Filter by author ptk1601 opened on Dec 3, 2024
  10

• Bug report [BUG] about tutorial

  aertslab/pycisTopic#186 · Filter by author Keep-Raining opened on Nov 5, 2024
  1

• fail to run AUCell_direct due to memory.

  aertslab/pycisTopic#184 · Filter by author JinKyu-Cheong opened on Nov 1, 2024

• Add pycisTopic images to DockerHub

  aertslab/pycisTopic#182 · Filter by author massonix opened on Oct 28, 2024
  1

• 1Tb memory is insufficient for normalize_scores

  aertslab/pycisTopic#179 · Filter by author JinKyu-Cheong opened on Oct 19, 2024
  8

• [Tutorial] [246] export_gene_activity_to_loom important in SCENIC+ analyses?

  aertslab/pycisTopic#177 · Filter by author yojetsharma opened on Oct 14, 2024
  1

• Feature request [FEATURE] DARs plotting options: is there a way to generate coverage plots instead of UMAP plots?

  aertslab/pycisTopic#175 · Filter by author yojetsharma opened on Oct 9, 2024

• export_pseudobulk about question

  aertslab/pycisTopic#174 · Filter by author sugiYag opened on Oct 9, 2024

• 'export_pseudobulk' output difference log

  aertslab/pycisTopic#172 · Filter by author GGboy-Zzz opened on Sep 23, 2024
  1

• pandas.errors.InvalidIndexError: Reindexing only valid with uniquely valued Index objects

  aertslab/pycisTopic#171 · Filter by author Quentin-bioinfo opened on Sep 19, 2024
  4