Issues

• Streaming dataset cache writes one .gtok file per item (doesn't scale on HPC)

  databio/geniml#21 · Filter by author nsheff opened on Jul 22, 2026
  1

• Standardize Atacformer and ScEmbed API

  enhancement
  databio/geniml#17 · Filter by author nleroy917 opened on Nov 4, 2025
  1

• geniml wont install with python 3.13

  databio/geniml#16 · Filter by author nleroy917 opened on Sep 29, 2025

• Deprecate .gtok files for now

  enhancement
  databio/geniml#14 · Filter by author nleroy917 opened on Sep 5, 2025

• Create a TokenizedCells class

  enhancementgood first issue
  databio/geniml#13 · Filter by author nleroy917 opened on Sep 5, 2025
  1

  

• Atacformer needs unit tests

  atacformer
  databio/geniml#11 · Filter by author nleroy917 opened on Aug 21, 2025

• Make the context_size configurable when running encode_tokenized_cells

  atacformerenhancement
  databio/geniml#10 · Filter by author nleroy917 opened on Aug 19, 2025

• Atacformer installation issues megathread

  atacformer
  databio/geniml#9 · Filter by author nleroy917 opened on Aug 19, 2025
  1

• tokenization of scEmbed

  databio/geniml#7 · Filter by author Keegan17123 opened on Nov 13, 2024
  5

• error in building model for likelihood (LH)

  databio/geniml#6 · Filter by author LimKaiShi opened on Oct 10, 2024

• Can bbclient module be its own package?

  databio/geniml#4 · Filter by author jkanche opened on Jul 15, 2024
  3