MANIFEST.in
README.md
requirements.txt
setup.py
geney/__init__.py
geney/api.py
geney/api_sections.py
geney/concurrent.py
geney/engine.py
geney/enrichment.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/models/.DS_Store
geney/models/openspliceai-mane/10000nt/model_10000nt_rs10.pt
geney/models/openspliceai-mane/10000nt/model_10000nt_rs11.pt
geney/models/openspliceai-mane/10000nt/model_10000nt_rs12.pt
geney/models/openspliceai-mane/10000nt/model_10000nt_rs13.pt
geney/models/openspliceai-mane/10000nt/model_10000nt_rs14.pt
geney/models/titer/bestmodel_0.pt
geney/models/titer/bestmodel_1.pt
geney/models/titer/bestmodel_10.pt
geney/models/titer/bestmodel_11.pt
geney/models/titer/bestmodel_12.pt
geney/models/titer/bestmodel_13.pt
geney/models/titer/bestmodel_14.pt
geney/models/titer/bestmodel_15.pt
geney/models/titer/bestmodel_16.pt
geney/models/titer/bestmodel_17.pt
geney/models/titer/bestmodel_18.pt
geney/models/titer/bestmodel_19.pt
geney/models/titer/bestmodel_2.pt
geney/models/titer/bestmodel_20.pt
geney/models/titer/bestmodel_21.pt
geney/models/titer/bestmodel_22.pt
geney/models/titer/bestmodel_23.pt
geney/models/titer/bestmodel_24.pt
geney/models/titer/bestmodel_25.pt
geney/models/titer/bestmodel_26.pt
geney/models/titer/bestmodel_27.pt
geney/models/titer/bestmodel_28.pt
geney/models/titer/bestmodel_29.pt
geney/models/titer/bestmodel_3.pt
geney/models/titer/bestmodel_30.pt
geney/models/titer/bestmodel_31.pt
geney/models/titer/bestmodel_4.pt
geney/models/titer/bestmodel_5.pt
geney/models/titer/bestmodel_6.pt
geney/models/titer/bestmodel_7.pt
geney/models/titer/bestmodel_8.pt
geney/models/titer/bestmodel_9.pt
geney/models/titer/dict_piror_front_Gaotrain.npy
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/engines.py
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/__init__.py
tests/benchmark_100.py
tests/benchmark_pipeline.py
tests/benchmark_screen.py
tests/conftest.py
tests/profile_pipeline.py
tests/test_api_contract.py
tests/test_enrichments.py
tests/test_failed_mutations.py
tests/test_mutation_pipeline.py
tests/test_screen.py