MANIFEST.in
README.md
pyproject.toml
requirements.txt
setup.py
geney/__init__.py
geney/api.py
geney/api_sections.py
geney/concurrent.py
geney/engine.py
geney/enrichment.py
geney/epistasis.py
geney/outcome_tree.py
geney/results.py
geney/screen.py
geney/screen_alphagenome.py
geney/transcript_tools.py
geney/utils.py
geney/variants.py
geney.egg-info/PKG-INFO
geney.egg-info/SOURCES.txt
geney.egg-info/dependency_links.txt
geney.egg-info/requires.txt
geney.egg-info/top_level.txt
geney/folding/__init__.py
geney/folding/codons.py
geney/folding/conserved.py
geney/folding/delta_mfe.py
geney/folding/pipeline.py
geney/folding/precompute.py
geney/folding/query.py
geney/folding/reference.py
geney/folding/vienna.py
geney/mirna/__init__.py
geney/mirna/au_params.json
geney/mirna/disruption.py
geney/mirna/expression.py
geney/mirna/features.py
geney/mirna/mibsim.py
geney/mirna/mibsim_params.json
geney/mirna/reference.py
geney/mirna/seed.py
geney/mirna/data/dashr2_expression.json
geney/mirna/data/mature.fa
geney/oncosplice/__init__.py
geney/oncosplice/align.py
geney/oncosplice/scoring.py
geney/pipelines/__init__.py
geney/pipelines/_batch.py
geney/pipelines/_common.py
geney/pipelines/_multi_transcript.py
geney/pipelines/_mutation.py
geney/pipelines/_splicing.py
geney/pipelines/_tis.py
geney/protein/__init__.py
geney/protein/analysis.py
geney/splicing/__init__.py
geney/splicing/branch_points.py
geney/splicing/engines.py
geney/splicing/ppt_scores.txt
geney/splicing/splice_graph.py
geney/splicing/transcripts.py
geney/tis/__init__.py
geney/tis/analysis.py
geney/tis/encoding.py
geney/tis/helpers.py
geney/tis/integration.py
geney/tis/metrics.py
geney/tis/model.py
geney/tis/prediction.py
geney/tis/visualization.py
geney/transcription/__init__.py
geney/transcription/encoding.py
geney/transcription/model.py
geney/transcription/pipeline.py
geney/transcription/prediction.py
geney/transcription/targets_human.txt
geney/visualization/__init__.py
geney/visualization/_folding.py
geney/visualization/_splicing.py
geney/visualization/_tis.py
geney/visualization/_transcription.py
geney/visualization/preview.py
tests/test_api_contract.py
tests/test_enrichments.py
tests/test_failed_mutations.py
tests/test_ground_truth.py
tests/test_mutation_pipeline.py
tests/test_screen.py