LICENSE
MANIFEST.in
README.md
pyproject.toml
pirlygenes/__init__.py
pirlygenes/cli.py
pirlygenes/cohorts.py
pirlygenes/coverage.py
pirlygenes/cta_curation_plots.py
pirlygenes/data_bundle.py
pirlygenes/data_inventory.py
pirlygenes/downloads.py
pirlygenes/gene_canonicalization.py
pirlygenes/gene_families.py
pirlygenes/gene_ids.py
pirlygenes/gene_names.py
pirlygenes/gene_sets_cancer.py
pirlygenes/load_dataset.py
pirlygenes/version.py
pirlygenes.egg-info/PKG-INFO
pirlygenes.egg-info/SOURCES.txt
pirlygenes.egg-info/dependency_links.txt
pirlygenes.egg-info/entry_points.txt
pirlygenes.egg-info/requires.txt
pirlygenes.egg-info/top_level.txt
pirlygenes/builders/__init__.py
pirlygenes/builders/affy_gpl570.py
pirlygenes/builders/gene_mapping.py
pirlygenes/builders/geo_matrix.py
pirlygenes/builders/ncbi_gene_info.py
pirlygenes/builders/recount3.py
pirlygenes/builders/source_data_mirror.py
pirlygenes/builders/treehouse.py
pirlygenes/cancer_types/__init__.py
pirlygenes/data/ADC-approved.csv
pirlygenes/data/ADC-trials.csv
pirlygenes/data/ADC-withdrawn.csv
pirlygenes/data/CAR-T-approved.csv
pirlygenes/data/TCR-T-approved.csv
pirlygenes/data/TCR-T-trials.csv
pirlygenes/data/artifact-expectations.csv
pirlygenes/data/bispecific-antibodies-approved.csv
pirlygenes/data/cancer-apd1-response.csv
pirlygenes/data/cancer-classification-ontology.csv
pirlygenes/data/cancer-code-burden-map.csv
pirlygenes/data/cancer-cohort-aggregates.csv
pirlygenes/data/cancer-compartment-panels.csv
pirlygenes/data/cancer-driver-genes.csv
pirlygenes/data/cancer-driver-variants.csv
pirlygenes/data/cancer-expression-source-candidates.csv
pirlygenes/data/cancer-family-panels.csv
pirlygenes/data/cancer-frameshift-burden.csv
pirlygenes/data/cancer-fusions.csv
pirlygenes/data/cancer-incidence-mortality.csv
pirlygenes/data/cancer-key-genes.csv
pirlygenes/data/cancer-lineage-group-overrides.csv
pirlygenes/data/cancer-lineage-groups.csv
pirlygenes/data/cancer-lineage-panels.csv
pirlygenes/data/cancer-reference-expression-samples.csv.gz
pirlygenes/data/cancer-subtype-groupings.csv
pirlygenes/data/cancer-supertype-panels.csv
pirlygenes/data/cancer-surfaceome.csv
pirlygenes/data/cancer-tmb.csv
pirlygenes/data/cancer-type-discriminators.csv
pirlygenes/data/cancer-type-genes.csv
pirlygenes/data/cancer-type-registry.csv
pirlygenes/data/cancer-viral-antigens.csv
pirlygenes/data/canonical-gene-reference.csv.gz
pirlygenes/data/cdna-identical-gene-groups.csv
pirlygenes/data/clean-tpm-censored-genes.csv
pirlygenes/data/cohort-registry.csv
pirlygenes/data/cta-protein-groups.csv
pirlygenes/data/culture-stress-genes.csv
pirlygenes/data/degenerate-subtype-pairs.csv
pirlygenes/data/degradation-gene-pairs.csv
pirlygenes/data/disease-state-rules.csv
pirlygenes/data/ensembl-gene-index.csv.gz
pirlygenes/data/ensembl-id-aliases.csv
pirlygenes/data/estimate-signatures.csv
pirlygenes/data/expression_sources.yaml
pirlygenes/data/extra-tx-mappings.csv
pirlygenes/data/ffpe-sensitive-markers.csv
pirlygenes/data/fusion-expression-effects.csv
pirlygenes/data/fusion-surrogate-expression.csv
pirlygenes/data/gene-list-provenance.csv
pirlygenes/data/gene-sets.csv
pirlygenes/data/heme-tumor-up-vs-matched-normal.csv
pirlygenes/data/hemoglobin-genes.csv
pirlygenes/data/histone-genes.csv
pirlygenes/data/housekeeping-genes.csv
pirlygenes/data/immune-receptor-segments.csv
pirlygenes/data/lineage-genes.csv
pirlygenes/data/mitochondrial-genes.csv
pirlygenes/data/multispecific-tcell-engager-trials.csv
pirlygenes/data/mutation-expression-effects.csv
pirlygenes/data/narrative-gene-sets.csv
pirlygenes/data/ncbi-symbol-synonyms.csv.gz
pirlygenes/data/nuclear-retained-lncrnas.csv
pirlygenes/data/numt-pseudogenes.csv
pirlygenes/data/protein-identical-gene-groups.csv
pirlygenes/data/proteoform-collapse-overrides.csv
pirlygenes/data/radioligand-targets.csv
pirlygenes/data/rare-cancer-fusion-rules.csv
pirlygenes/data/rare-cancer-rna-surrogates.csv
pirlygenes/data/ribosomal-protein-genes.csv
pirlygenes/data/ribosomal-protein-pseudogenes.csv
pirlygenes/data/rrna-and-pseudogenes.csv
pirlygenes/data/sequence-identical-gene-groups.csv
pirlygenes/data/small-noncoding-rnas.csv
pirlygenes/data/stem-cell-marker-panels.csv
pirlygenes/data/surface-proteins.csv
pirlygenes/data/therapy-benefit-toxicity-evidence.csv
pirlygenes/data/therapy-response-signatures.csv
pirlygenes/data/tme-markers.csv
pirlygenes/data/tumor-up-vs-matched-normal.csv
pirlygenes/expression/__init__.py
pirlygenes/expression/accessors.py
pirlygenes/expression/aggregate.py
pirlygenes/expression/normalize.py
pirlygenes/expression/protein_groups.py
pirlygenes/expression/qc.py
pirlygenes/expression/representatives.py
pirlygenes/expression/source_cohort_origin.py
pirlygenes/expression/stats.py
tests/test_apl_subtype_key_genes.py
tests/test_build_treehouse.py
tests/test_builders_parsers.py
tests/test_cancer_apd1_response.py
tests/test_cancer_burden.py
tests/test_cancer_frameshift_burden.py
tests/test_cancer_fusions.py
tests/test_cancer_subtype_groupings.py
tests/test_cancer_tmb.py
tests/test_cancer_type_registry.py
tests/test_cancer_types.py
tests/test_cancer_viral_antigens.py
tests/test_citation_integrity.py
tests/test_clean_tpm_shared.py
tests/test_cohort_aggregates.py
tests/test_cohort_expression_views.py
tests/test_cohort_gene_percentiles.py
tests/test_cohort_registry.py
tests/test_cohorts_registry.py
tests/test_coverage.py
tests/test_cta_curation_plots.py
tests/test_downloads_and_cli.py
tests/test_expression.py
tests/test_format_cancer_code_label.py
tests/test_gene_canonicalization.py
tests/test_gene_families.py
tests/test_gene_family_generator.py
tests/test_gene_ids.py
tests/test_gene_ids_unit.py
tests/test_gene_mapping.py
tests/test_load_dataset_and_gene_sets.py
tests/test_ntrk_tumor_agnostic.py
tests/test_ontology_integrity.py
tests/test_pan_cancer_expression_integrity.py
tests/test_pool_cohort_samples.py
tests/test_protein_identical_groups.py
tests/test_readme_count_claims.py
tests/test_readme_imports.py
tests/test_recount3_normalize.py
tests/test_reference_format.py
tests/test_reference_union_heterogeneity.py
tests/test_registry_completeness.py
tests/test_registry_expression_consistency.py
tests/test_representative_samples.py
tests/test_sarc_subtype_key_genes.py
tests/test_sarcoma_lineage.py
tests/test_source_cohort_origin.py
tests/test_stats_and_data.py
tests/test_therapy_benefit_toxicity_evidence.py
tests/test_tranche_c_key_genes.py