Source Modules (src/)

The src/ package contains all reusable pipeline components. Each module is independently testable and has a corresponding test file under unittests/.

Module summary

Module	Class(es)	Role
data_loader	DataLoader	Load Atlas counts, metadata, and query files
normalization	FrequencyNormalizer, DESeq2Normalizer	Two normalization strategies
preprocessing	Preprocessor	Gene filtering, stratification, outlier detection
bayesage2	BayesAge2Clock	BayesAge 2.0 — Poisson log-likelihood clock
elastic_net	ElasticNetClock	Elastic Net regularized regression
pcr	PCRClock	Principal Component Regression
gene_mapping	GeneMapper	Ensembl ENSNFUG IDs → Atlas gene names
calibration	QueryCountExtractor, CalibrationManager	End-to-end clock application to query data

Data flow

DataLoader ──► Preprocessor ──► (FrequencyNormalizer) ──► BayesAge2Clock
                     │
                     └──────► (DESeq2Normalizer) ──► PCRClock
                                                  └──► ElasticNetClock

QueryCountExtractor ──► GeneMapper ──► correct_batch ──► CalibrationManager

Tests

pytest unittests/ -v

Eight test files cover all modules:

unittests/
  test_data_loader.py
  test_normalization.py
  test_preprocessing.py
  test_bayesage2.py
  test_elastic_net.py
  test_pcr.py
  test_run_clocks.py