Issues

• BUG: loop reconstruction sometimes generate oddly shaped loops

  stanfish06/scloop#99 · Filter by author stanfish06 opened on Jul 22, 2026

• TODO: integrate image-based registration into cross-matching

  stanfish06/scloop#98 · Filter by author stanfish06 opened on Jul 14, 2026

• TODO: on-loop slope field estimation and trajectory fitting with mellon

  stanfish06/scloop#95 · Filter by author stanfish06 opened on Jun 27, 2026

• Collection of ideas

  stanfish06/scloop#87 · Filter by author stanfish06 opened on Apr 21, 2026
  10

• TODO: lazy loading of modules

  stanfish06/scloop#85 · Filter by author stanfish06 opened on Apr 21, 2026

• TODO: refine trajectory fitting module

  stanfish06/scloop#84 · Filter by author stanfish06 opened on Apr 15, 2026

• TODO: setup benchmark suite

  stanfish06/scloop#83 · Filter by author stanfish06 opened on Apr 6, 2026
  1

• BUG: type handling in loops function in _homology pl module

  stanfish06/scloop#81 · Filter by author stanfish06 opened on Mar 12, 2026

• TODO: implement diffusion map and remove scanpy dep

  stanfish06/scloop#78 · Filter by author stanfish06 opened on Mar 6, 2026
  4

• TODO: more visualization approaches, such as tree view with loops, etc

  stanfish06/scloop#77 · Filter by author stanfish06 opened on Mar 6, 2026

• TODO: metric selection + normalization for Hodge embedding

  stanfish06/scloop#76 · Filter by author stanfish06 opened on Mar 6, 2026

• BUG: find_loops failed with too small homology threshold

  stanfish06/scloop#75 · Filter by author stanfish06 opened on Feb 23, 2026

• TODO: save objects to h5ad

  stanfish06/scloop#74 · Filter by author stanfish06 opened on Feb 8, 2026
  1

• ISSUE: prepare logic, if use scvi, feature selection shouldnt be needed

  stanfish06/scloop#73 · Filter by author stanfish06 opened on Feb 4, 2026

• BUG: prepare error crash kernel

  stanfish06/scloop#72 · Filter by author stanfish06 opened on Feb 4, 2026

• BUG: trajectory overlay function failed with basis other than diffmap

  stanfish06/scloop#71 · Filter by author stanfish06 opened on Feb 4, 2026

• TODO: visualization of statistical test

  stanfish06/scloop#69 · Filter by author stanfish06 opened on Jan 28, 2026

• ISSUE: permutation test is slow

  stanfish06/scloop#67 · Filter by author stanfish06 opened on Jan 21, 2026

• TODO: try induced homology for cross matching

  stanfish06/scloop#66 · Filter by author stanfish06 opened on Jan 21, 2026

• TODO: better handling of embedding key in prepare.py

  stanfish06/scloop#65 · Filter by author stanfish06 opened on Jan 19, 2026

• TODO: increase randomness of herding

  stanfish06/scloop#64 · Filter by author stanfish06 opened on Jan 18, 2026

• TODO: add doc

  stanfish06/scloop#63 · Filter by author stanfish06 opened on Jan 18, 2026

• TODO: compute divergence

  stanfish06/scloop#62 · Filter by author stanfish06 opened on Jan 17, 2026

• TODO: add more tests

  stanfish06/scloop#61 · Filter by author stanfish06 opened on Jan 14, 2026

• TODO: make bootstrap more robust

  stanfish06/scloop#59 · Filter by author stanfish06 opened on Jan 7, 2026
  1