├── Dockerfile ├── LICENSE ├── LICENSE_snfpy ├── NOTICE ├── README.md ├── datasources ├── README.md ├── acmg │ ├── README.md │ └── acmg.secondaryfindings.v3.txt ├── cancergenecensus │ ├── README.md │ ├── cancer_gene_census_empty.genes.tsv │ ├── diff_versions.py │ └── extract_genes.py ├── cancerhotspots │ ├── README.md │ ├── hotspots.txt │ ├── hotspots3d.txt │ ├── hotspots_v2.txt │ └── prep_3dhotspots │ │ ├── 3d_hotspots.xls │ │ ├── 3d_hotspots_T2.txt │ │ ├── 3d_hotspots_T5.txt │ │ └── prep3dhotspots.py ├── clinvar │ ├── README.md │ ├── prepare_clinvar.py │ └── variant_summary.lite.txt ├── cosmic │ ├── CosmicMutantExport_empty.lite.txt │ ├── README.md │ └── prepare_cosmic.py ├── exac │ ├── README.md │ ├── build_exac.sh │ ├── exac.expanded.r1.empty.txt │ └── expand_exac.py ├── gsea_gene_sets │ ├── GSEA_cancer_gene_sets.txt │ ├── README.md │ └── c4.cm.v6.0.symbols.txt ├── hereditary │ ├── README.md │ └── hereditary.txt ├── lawrence │ ├── README.md │ ├── lawrence_ST2.txt │ ├── lawrence_mapped_ontology.txt │ └── map_oncotree_lawrence.ipynb ├── moalmanac │ ├── README.md │ ├── create_almanac_db.py │ └── molecular-oncology-almanac.json ├── oncotree │ ├── README.md │ ├── get_oncotree.py │ └── oncotree.2023-03-09.txt └── preclinical │ ├── README.md │ ├── almanac-gdsc-mappings.json │ ├── annotated │ ├── README.md │ ├── annotate-copy-numbers.py │ ├── annotate-fusions.py │ ├── annotate-molecular-features.sh │ ├── annotate-variants.py │ ├── cell-lines.copy-numbers.annotated.txt │ ├── cell-lines.fusions.annotated.gene1.txt │ ├── cell-lines.fusions.annotated.gene2.txt │ ├── cell-lines.fusions.annotated.txt │ └── cell-lines.somatic-variants.annotated.txt │ ├── cell-lines.pkl │ ├── formatted │ ├── 0.map-almanac-to-gdsc.ipynb │ ├── 1.process-cell-line-molecular-features.ipynb │ ├── README.md │ ├── almanac-gdsc-mappings.json │ ├── cell-line-names.formatted.txt │ ├── cell-lines.copy-numbers.txt │ ├── cell-lines.fusions.txt │ ├── cell-lines.somatic-variants.txt │ ├── cell-lines.summary.txt │ └── sanger.gdsc.txt │ ├── generate-dictionary.ipynb │ └── source │ ├── README.md │ ├── ccle-2019 │ └── README.md │ ├── depmap │ └── README.md │ └── gdsc │ └── README.md ├── docs ├── README.md ├── description-of-inputs.md ├── description-of-outputs.md ├── how-to-contribute.md ├── pull_request_template.md └── template-release.md ├── example_data ├── README.md ├── example_patient.capture.germline.maf ├── example_patient.capture.sbs_contributions.txt ├── example_patient.capture.somatic.called.cna.txt ├── example_patient.capture.somatic.coverage.txt ├── example_patient.capture.somatic.indels.maf ├── example_patient.capture.somatic.seg.annotated ├── example_patient.capture.somatic.snvs.maf ├── example_patient.rna.somatic.snvs.maf ├── example_patient.rna.star.fusions.txt ├── example_patient.simplified_input.txt └── manufacture-germline-input.ipynb ├── example_output ├── README.md ├── example.input-metadata.txt ├── example.log ├── example.moalmanac-execution.json ├── example_output.BRAF p.V600E (Missense).Dabrafenib.png ├── example_output.BRAF p.V600E (Missense).Trametinib ├── example_output.COL1A1--CITED4 Fusion.Imatinib.png ├── example_output.actionable.txt ├── example_output.germline.acmg.txt ├── example_output.germline.cancer_related.txt ├── example_output.germline.hereditary_cancers.txt ├── example_output.integrated.summary.txt ├── example_output.matchmaker.txt ├── example_output.msi_variants.txt ├── example_output.mutational_burden.txt ├── example_output.preclinical_efficacy.txt ├── example_output.report.html ├── example_output.somatic.filtered.txt ├── example_output.somatic.scored.txt ├── example_output.therapeutic_strategies.txt └── example_output.validation_overlap.png ├── moalmanac ├── README.md ├── __init__.py ├── annotation-databases.ini ├── annotator.py ├── colnames.ini ├── config.ini ├── config.py ├── datasources.py ├── evaluator.py ├── features.py ├── illustrator.py ├── investigator.py ├── logger.py ├── matchmaker.py ├── moalmanac.py ├── ontologymapper.py ├── preclinical-databases.ini ├── reader.py ├── reporter.py ├── run_4x_for_output_regression_test.py ├── run_example.py ├── run_output_regression_test.py ├── run_unit_tests.sh ├── simplified_input.py ├── snf.py ├── templates │ ├── disclaimer.html │ ├── footer.html │ ├── header.html │ ├── index.html │ ├── logo.html │ ├── metadata.html │ ├── modals │ │ ├── bins.html │ │ ├── cell_line_info.html │ │ ├── datasources.html │ │ ├── efficacy.html │ │ ├── evidence_prognosis.html │ │ ├── evidence_resistance.html │ │ ├── evidence_sensitive.html │ │ ├── levels.html │ │ ├── link_modals.html │ │ ├── table_preclinical.html │ │ └── text_preclinical.html │ ├── report_table │ │ ├── columns_biological.html │ │ ├── columns_prognosis.html │ │ ├── columns_therapies.html │ │ ├── table.html │ │ ├── table_biological.html │ │ ├── table_prognostic.html │ │ ├── table_resistance.html │ │ ├── table_sensitive.html │ │ └── table_similarity.html │ └── static │ │ ├── css │ │ ├── bootstrap3.min.css 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