.gitignore
CLAUDE.md
LICENSE
MANIFEST.in
README.md
build-docs.sh
deploy.sh
develop.sh
format.sh
lint.sh
pyproject.toml
test.sh
.github/workflows/tests.yml
docs/analyze-api.md
docs/analyze-command.md
docs/cta-curation.md
docs/cta-deflated-frac-dist.png
docs/cta-filter-funnel.png
docs/cta-filter-outcome.png
docs/cta-protein-vs-rna.png
docs/cta-source-venn.png
docs/embedding-gene-selection.md
docs/expression-data-audit.md
docs/expression-data-refresh-plan.md
docs/expression-sources-per-code.md
docs/figure-audit.md
docs/gene-sets.md
docs/lineage-aware-decomposition.md
docs/reasoning-pipeline.md
docs/step0-reasoning.md
notebooks/Add alias column and rename columns.ipynb
notebooks/Generate CTA list CSV.ipynb
notebooks/Import ADC trials CSV.ipynb
notebooks/PanCancer_ADC_trials_supp5.csv
notebooks/cancer-driver-genes.csv
notebooks/cancer-driver-variants.csv
notebooks/cancer-testis-antigens.csv
notebooks/class1-mhc-presentation-pathway.csv
notebooks/ewsr1-fli1-ct-genes-hpa.ipynb
notebooks/interferon-response.csv
pirlygenes/__init__.py
pirlygenes/cli.py
pirlygenes/data_bundle.py
pirlygenes/data_inventory.py
pirlygenes/downloads.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/geo_matrix.py
pirlygenes/builders/ncbi_gene_info.py
pirlygenes/builders/treehouse.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pirlygenes/data/ADC-withdrawn.csv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-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-key-genes.csv
pirlygenes/data/cancer-lineage-panels.csv
pirlygenes/data/cancer-reference-expression-samples.csv.gz
pirlygenes/data/cancer-surfaceome.csv
pirlygenes/data/cancer-testis-antigens.csv
pirlygenes/data/cancer-type-genes.csv
pirlygenes/data/cancer-type-registry.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-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-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/nuclear-retained-lncrnas.csv
pirlygenes/data/numt-pseudogenes.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/small-noncoding-rnas.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/qc.py
pirlygenes/expression/source_cohort_origin.py
pirlygenes/expression/stats.py
reports/cross-modality-target-report-2026-04.md
scripts/audit_therapy_path_curation.py
scripts/backfill_tumor_origin.py
scripts/build_beataml_reference_expression.py
scripts/build_bl_gdc_reference_expression.py
scripts/build_chon_reference_expression.py
scripts/build_cllmap_reference_expression.py
scripts/build_ctcl_scrna_reference_expression.py
scripts/build_geo_heme_reference_expression.py
scripts/build_geo_matrix.py
scripts/build_gpl570_microarray.py
scripts/build_gse98894_midgut_net.py
scripts/build_lnen_drmetrics_reference_expression.py
scripts/build_mbl_subgroups_marker_classifier.py
scripts/build_mmrf_reference_expression.py
scripts/build_pannet_reference_expression.py
scripts/build_sclc_reference_expression.py
scripts/build_sclc_subtypes_tf_dominance.py
scripts/build_target_all_reference_expression.py
scripts/build_target_subprojects.py
scripts/build_treehouse_reference_expression.py
scripts/generate_gene_family_sets.py
scripts/import_cancer_specific_expression.py
scripts/reshard_tcga_subset.py
scripts/sweep_sarc_rare_subtypes.py
scripts/sweep_treehouse_polya_cohorts.py
scripts/sweep_treehouse_ribod_cohorts.py
scripts/sweep_treehouse_sarc_subtypes.py
scripts/sweep_treehouse_tcga_brca_pam50.py
scripts/sweep_treehouse_tcga_cohorts.py
scripts/sweep_treehouse_tcga_glioma_split.py
scripts/sweep_treehouse_tcga_hnsc_hpv.py
scripts/sweep_treehouse_tcga_luad_mutations.py
tests/expr.png
tests/pfo002-summary.png
tests/pfo002-treatments.png
tests/test_apl_subtype_key_genes.py
tests/test_build_treehouse.py
tests/test_builders_parsers.py
tests/test_cancer_type_registry.py
tests/test_downloads_and_cli.py
tests/test_expression.py
tests/test_gene_families.py
tests/test_gene_ids.py
tests/test_gene_ids_unit.py
tests/test_load_dataset_and_gene_sets.py
tests/test_readme_imports.py
tests/test_registry_completeness.py
tests/test_sarc_subtype_key_genes.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