21096138363

Committed 17 Jan 2026 02:54PM UTC coverage: 45.067% (-9.0%) from 54.087%

Build # 21096138363

Build Type

push

github

Committed by

iskandr

Commit Message

Add Amplify, GEX, and Unify modules for multi-experiment analysis

New modules:
- amplify.py: Load Amplify platform data with SNR/quality filtering
- gex.py: Flexible gene expression augmentation from 10x HDF5 files
- unify.py: Merge clonotype data from multiple experiments

New CLI commands:
- load-amplify: Load Amplify Excel files with quality flags
- unify: Merge multiple clonotype files with occurrence tracking

Updates:
- Sample sheet: Support amplify_path, gex_path, experiment fields
- Config: Add AmplifyConfig, GEXConfig, UnifyConfig classes
- README: Add algorithmic details for all pipeline steps
- Tests: Update to use new alpha_leader/beta_leader API

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

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