.gitignore
LICENSE
README.md
build-docs.sh
deploy.sh
develop.sh
format.sh
lint.sh
pyproject.toml
test.sh
.github/workflows/tests.yml
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/gene-sets.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/PLAN-1.4.0-radioligand.md
pirlygenes/__init__.py
pirlygenes/aggregate_gene_expression.py
pirlygenes/cli.py
pirlygenes/common.py
pirlygenes/gene_ids.py
pirlygenes/gene_names.py
pirlygenes/gene_sets_cancer.py
pirlygenes/load_dataset.py
pirlygenes/load_expression.py
pirlygenes/plot.py
pirlygenes/plot_data_helpers.py
pirlygenes/sample_context.py
pirlygenes/sample_quality.py
pirlygenes/therapy_response.py
pirlygenes/transcript_to_gene.py
pirlygenes/tumor_purity.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/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pirlygenes/data/ADC-withdrawn.csv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/bispecific-antibodies-approved.csv
pirlygenes/data/cancer-driver-genes.csv
pirlygenes/data/cancer-driver-variants.csv
pirlygenes/data/cancer-family-panels.csv
pirlygenes/data/cancer-surfaceome.csv
pirlygenes/data/cancer-testis-antigens.csv
pirlygenes/data/cancer-type-genes.csv
pirlygenes/data/culture-stress-genes.csv
pirlygenes/data/degradation-gene-pairs.csv
pirlygenes/data/ensembl-id-aliases.csv
pirlygenes/data/estimate-signatures.csv
pirlygenes/data/extra-tx-mappings.csv
pirlygenes/data/ffpe-sensitive-markers.csv
pirlygenes/data/gene-sets.csv
pirlygenes/data/housekeeping-genes.csv
pirlygenes/data/hpa-cell-type-expression.csv
pirlygenes/data/lineage-genes.csv
pirlygenes/data/mitochondrial-genes.csv
pirlygenes/data/multispecific-tcell-engager-trials.csv
pirlygenes/data/pan-cancer-expression.csv
pirlygenes/data/radioligand-targets.csv
pirlygenes/data/surface-proteins.csv
pirlygenes/data/therapy-response-signatures.csv
pirlygenes/data/tme-markers.csv
pirlygenes/decomposition/__init__.py
pirlygenes/decomposition/engine.py
pirlygenes/decomposition/panels.py
pirlygenes/decomposition/plot.py
pirlygenes/decomposition/signature.py
pirlygenes/decomposition/templates.py
reports/cross-modality-target-report-2026-04.md
tests/expr.png
tests/pfo002-summary.png
tests/pfo002-treatments.png
tests/test_aggregate_gene_expression.py
tests/test_analyze_redundancy.py
tests/test_cli_output_cleanup.py
tests/test_common_gene_names.py
tests/test_decomposition.py
tests/test_gene_ids.py
tests/test_gene_ids_unit.py
tests/test_load_dataset_and_gene_sets.py
tests/test_load_expression.py
tests/test_matched_normal.py
tests/test_normalization_comparison.py
tests/test_perf_regression.py
tests/test_plot_and_cli.py
tests/test_plot_data_helpers.py
tests/test_report_clarity_and_met_site.py
tests/test_sample_context.py
tests/test_sample_quality.py
tests/test_therapy_response.py
tests/test_tumor_expression.py
tests/test_tumor_purity_symbol_build.py
tests/test_v42_sample_context_propagation.py