.gitattributes
.gitignore
Dockerfile
LICENSE
README.md
config_example_full.yaml
environment.yml
logo-full.jpeg
logo.jpeg
pyproject.toml
test_assets.py
.github/copilot-instructions.md
.github/workflows/release.yml
conda-recipe/meta.yaml
conda-recipe-dge/meta.yaml
config/config.yaml
config/config_unified.yaml
src/config/bwq_config.yaml
src/config/example_bwq_config.yaml
src/config/optimizer_final_flync_ebm.yaml
src/data/X_test.parquet
src/data/X_train.parquet
src/data/X_val.parquet
src/data/ncr_base.gtf
src/data/pcg_base.gtf
src/data/cv_artifacts/aggregated_metrics_summary.json
src/data/cv_artifacts/confusion_matrices_per_fold.csv
src/data/cv_artifacts/final_feature_importances.csv
src/data/cv_artifacts/metrics_per_fold.csv
src/data/cv_artifacts/pr_curve_points.csv
src/data/cv_artifacts/roc_curve_points.csv
src/data/holdout_artifacts/holdout_confusion_matrix.csv
src/data/holdout_artifacts/holdout_confusion_matrix_normalized.csv
src/data/holdout_artifacts/holdout_feature_importances.csv
src/data/holdout_artifacts/holdout_metrics.csv
src/data/holdout_artifacts/holdout_pr_curve.csv
src/data/holdout_artifacts/holdout_roc_curve.csv
src/flync/__init__.py
src/flync/_version.py
src/flync/api.py
src/flync/cli.py
src/flync.egg-info/PKG-INFO
src/flync.egg-info/SOURCES.txt
src/flync.egg-info/dependency_links.txt
src/flync.egg-info/entry_points.txt
src/flync.egg-info/requires.txt
src/flync.egg-info/top_level.txt
src/flync/assets/__init__.py
src/flync/assets/flync_ebm_model.pkl
src/flync/assets/flync_ebm_model_HOLDOUT.pkl
src/flync/assets/flync_ebm_model_params.json
src/flync/assets/flync_ebm_model_schema.json
src/flync/assets/flync_ebm_scaler.pkl
src/flync/config/__init__.py
src/flync/config/bwq_config.yaml
src/flync/features/README.md
src/flync/features/__init__.py
src/flync/features/bwq.py
src/flync/features/feature_cleaning.py
src/flync/features/feature_wrapper.py
src/flync/features/kmer.py
src/flync/features/mfe.py
src/flync/ml/__init__.py
src/flync/ml/ebm_predictor.py
src/flync/ml/example_usage.py
src/flync/ml/extract_model_schema.py
src/flync/ml/predict_test.py
src/flync/ml/predictor.py
src/flync/ml/schema_extractor.py
src/flync/ml/schema_validator.py
src/flync/optimizer/README.md
src/flync/optimizer/__init__.py
src/flync/optimizer/batch_optimization.py
src/flync/optimizer/hyperparameter_optimizer.py
src/flync/utils/__init__.py
src/flync/utils/kmer_redux.py
src/flync/utils/progress.py
src/flync/utils/util_sparse_to_parquet.py
src/flync/workflows/Snakefile
src/flync/workflows/rules/assembly.smk
src/flync/workflows/rules/dge.smk
src/flync/workflows/rules/mapping.smk
src/flync/workflows/rules/merge.smk
src/flync/workflows/rules/quantify.smk
src/flync/workflows/scripts/ballgown_dge.R
src/flync/workflows/scripts/predownload_tracks.py
src/notebooks/1_preprocess_genome_gtf.ipynb
src/notebooks/2_training_data.ipynb
src/notebooks/3_model_ebm_holdout.ipynb
src/notebooks/4_model_ebm_final.ipynb
src/notebooks/lazypredict_redux.csv
test/config.yaml
test/config_auto.yaml
test/config_local_fastq.yaml
test/config_simple.yaml
test/metadata.csv
test/samples.txt