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Add Logistic PCA (LPCA) analysis - #500

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Jeebjean wants to merge 29 commits into

Reed-CompBio:mainfrom

Jeebjean:lpca-integration

Open

Add Logistic PCA (LPCA) analysis#500
Jeebjean wants to merge 29 commits into
Reed-CompBio:mainfrom
Jeebjean:lpca-integration

Commits on Jul 10, 2026
- Add Logistic PCA (LPCA) analysis
  Jeebjean
  committed
  1e9b218
- Add LPCA Docker wrapper
  Jeebjean
  committed
  bb338a8
Commits on Jul 21, 2026
- Add unit tests for LPCA analysis
  Jeebjean
  committed
  efd1005
- Add LPCA visualization: generate lpca.png and lpca-coordinates.txt
  Jeebjean
  committed
  8f89119
- Increase Docker timeout to 600s for large LPCA matrices
  Jeebjean
  committed
  3d9a38f
- Restore config.yaml to main defaults, keep only lpca block
  Jeebjean
  committed
  e4b4679
- Skip LPCA tests if Docker image not available
  Jeebjean
  committed
  41b64b7
Commits on Jul 23, 2026
- Add rARPACK for memory-efficient LPCA with partial_decomp=TRUE
  Jeebjean
  committed
  c49362f
Commits on Jul 27, 2026
Commits on Jul 30, 2026
Commits on Sep 29, 2026
- Add robustness to LPCA R wrapper and test code
  agitter
  committed
  2ced8af
Commits on Oct 1, 2026
- Refactor LPCA wrapper and tests
  agitter
  committed
  e1c0be2
- Add tests, refactor config and Snakefile
  agitter
  committed
  e2c91d2
Commits on Oct 2, 2026
- Formatting and doc cleanup
  agitter
  committed
  2d7d91c
- Config whitespace
  agitter
  committed
  894643d
- Update comments
  agitter
  committed
  f2a24f4
Commits on Oct 4, 2026
- Memory discussions
  agitter
  committed
  415c799
- Disable LPCA by default
  agitter
  committed
  7100ada