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ISSUE: permutation test is slow

Status: Open.

#67 In stanfish06/scloop;

· stanfish06 opened on Jan 21, 2026

TODO: try induced homology for cross matching

Status: Open.

#66 In stanfish06/scloop;

· stanfish06 opened on Jan 21, 2026

TODO: better handling of embedding key in prepare.py

Status: Open.

#65 In stanfish06/scloop;

· stanfish06 opened on Jan 19, 2026

TODO: increase randomness of herding

Status: Open.

#64 In stanfish06/scloop;

· stanfish06 opened on Jan 18, 2026

TODO: add doc

Status: Open.

#63 In stanfish06/scloop;

· stanfish06 opened on Jan 18, 2026

TODO: compute divergence

Status: Open.

#62 In stanfish06/scloop;

· stanfish06 opened on Jan 17, 2026

TODO: add more tests

Status: Open.

#61 In stanfish06/scloop;

· stanfish06 opened on Jan 14, 2026

TODO: make bootstrap more robust

Status: Open.

#59 In stanfish06/scloop;

· stanfish06 opened on Jan 7, 2026

ISSUE: neural net cross matching unstable

Status: Open.

#56 In stanfish06/scloop;

· stanfish06 opened on Jan 5, 2026

ISSUE: unstable trajectory and gene trends

Status: Open.

#55 In stanfish06/scloop;

· stanfish06 opened on Jan 4, 2026

Rich console does not print SUCCESS in jupyter notebook

Status: Open.

#52 In stanfish06/scloop;

· stanfish06 opened on Jan 3, 2026

TODO: merge redundant loop classes

Status: Open.

#46 In stanfish06/scloop;

· stanfish06 opened on Jan 1, 2026