LICENSE
MANIFEST.in
README.md
pyproject.toml
pirl_trufflepig.egg-info/PKG-INFO
pirl_trufflepig.egg-info/SOURCES.txt
pirl_trufflepig.egg-info/dependency_links.txt
pirl_trufflepig.egg-info/entry_points.txt
pirl_trufflepig.egg-info/requires.txt
pirl_trufflepig.egg-info/top_level.txt
tests/test_agent_metadata_clause.py
tests/test_aggregate_gene_expression.py
tests/test_analyze_api.py
tests/test_analyze_redundancy.py
tests/test_analyze_reports_script.py
tests/test_aneuploidy_axis.py
tests/test_apl_subtype_key_genes.py
tests/test_apply_cancer_type_evidence.py
tests/test_battery_audit_fixes.py
tests/test_brief.py
tests/test_calibration_subtype_match.py
tests/test_cancer_ontology_resolve.py
tests/test_cancer_type_centroid.py
tests/test_cancer_type_context.py
tests/test_cancer_type_evidence.py
tests/test_cancer_type_ontology.py
tests/test_cancer_type_registry.py
tests/test_clean_tpm_v4.py
tests/test_cli_narrative.py
tests/test_cli_output_cleanup.py
tests/test_cli_scaffold.py
tests/test_cohort_deconvolve.py
tests/test_common_ranges_cache.py
tests/test_confidence.py
tests/test_decomposition.py
tests/test_decomposition_internals.py
tests/test_degenerate_subtype.py
tests/test_disease_state_rules.py
tests/test_ensg_aware_qc.py
tests/test_evidence_table_concordance.py
tests/test_evidence_tables.py
tests/test_expression_classifier.py
tests/test_expression_decomposition.py
tests/test_expression_qc_lncrna.py
tests/test_extra_tx_mappings.py
tests/test_family_panel_ensg_scoring.py
tests/test_family_qc_contract.py
tests/test_format.py
tests/test_gene_ids.py
tests/test_gene_ids_unit.py
tests/test_healthy_vs_tumor.py
tests/test_issue_152_pannet_cohort.py
tests/test_issue_158_metabolic_axes.py
tests/test_issue_160_orphan_family_dominance.py
tests/test_issue_161_degenerate_ci.py
tests/test_issue_162_lineage_specificity.py
tests/test_issue_169_call_confidence.py
tests/test_issue_170_lineage_panel_floor.py
tests/test_issue_171_mixture_cohort.py
tests/test_issue_51_sarc_matched_normal.py
tests/test_issue_56_subtype_refinement.py
tests/test_issue_58_extended_tme.py
tests/test_issue_59_optional_compartments.py
tests/test_issue_59_sm_leakage.py
tests/test_lineage_evidence.py
tests/test_lineage_gate_wired_live.py
tests/test_lineage_marker_recall.py
tests/test_lineage_panel_selector.py
tests/test_literature_signatures.py
tests/test_load_dataset_and_gene_sets.py
tests/test_load_expression.py
tests/test_local_reference_veto.py
tests/test_longitudinal_deltas.py
tests/test_matched_normal.py
tests/test_matched_normal_cell_type.py
tests/test_median_battery_classification.py
tests/test_no_figures_restore.py
tests/test_normal_tissue_tiebreaker.py
tests/test_normalization_comparison.py
tests/test_offcontext_targets.py
tests/test_output_dir_lock.py
tests/test_perf_regression.py
tests/test_plot_and_cli.py
tests/test_plot_data_helpers.py
tests/test_plot_purity_methods.py
tests/test_plot_reference_lines.py
tests/test_plot_therapy_pathway_state.py
tests/test_prad_stromal_pitfall.py
tests/test_proteoform_key_space.py
tests/test_provenance.py
tests/test_purity_internals.py
tests/test_reasoning_rules.py
tests/test_regenerate_local_reports.py
tests/test_registry_completeness.py
tests/test_report_clarity_and_met_site.py
tests/test_rna_qc.py
tests/test_robust_attribution.py
tests/test_sample_context.py
tests/test_sample_context_edges.py
tests/test_sample_quality.py
tests/test_sarc_subtype_key_genes.py
tests/test_signal_views.py
tests/test_signature_detection_floor.py
tests/test_subtype_deconvolved_refs.py
tests/test_target_deep_dive.py
tests/test_taxonomy_robustness.py
tests/test_tcga_decompose.py
tests/test_tcga_deconvolved_expression.py
tests/test_therapeutic_agents.py
tests/test_therapy_path_curation.py
tests/test_therapy_response.py
tests/test_tnbc_basal_brca_rescue.py
tests/test_tranche_c_key_genes.py
tests/test_tumor_expression.py
tests/test_tumor_purity_reference.py
tests/test_tumor_purity_symbol_build.py
tests/test_tumor_type_ontology.py
tests/test_v42_sample_context_propagation.py
tests/test_web.py
trufflepig/__init__.py
trufflepig/_data.py
trufflepig/aggregate_gene_expression.py
trufflepig/alteration_effects.py
trufflepig/alterations.py
trufflepig/aneuploidy_axis.py
trufflepig/brief.py
trufflepig/cancer_ontology.py
trufflepig/cancer_type_centroid.py
trufflepig/cancer_type_evidence.py
trufflepig/cancer_type_ontology.py
trufflepig/clean_tpm.py
trufflepig/cli.py
trufflepig/cohort_deconvolve.py
trufflepig/common.py
trufflepig/confidence.py
trufflepig/degenerate_subtype.py
trufflepig/disease_state_rules.py
trufflepig/evidence_tables.py
trufflepig/expression_classifier.py
trufflepig/expression_decomposition.py
trufflepig/expression_normalize.py
trufflepig/expression_qc.py
trufflepig/feature_spaces.py
trufflepig/format.py
trufflepig/fusion_effects.py
trufflepig/fusions.py
trufflepig/healthy_vs_tumor.py
trufflepig/hla.py
trufflepig/lineage_evidence.py
trufflepig/lineage_marker_recall.py
trufflepig/lineage_panels.py
trufflepig/literature_signatures.py
trufflepig/load_expression.py
trufflepig/main.py
trufflepig/normalization_usage.py
trufflepig/pipeline.py
trufflepig/plot.py
trufflepig/plot_context.py
trufflepig/plot_data_helpers.py
trufflepig/plot_embedding.py
trufflepig/plot_reference_lines.py
trufflepig/plot_scatter.py
trufflepig/plot_strip.py
trufflepig/plot_subtype_signature.py
trufflepig/plot_target_deep_dive.py
trufflepig/plot_therapy.py
trufflepig/plot_tumor_expr.py
trufflepig/provenance.py
trufflepig/purity_calibration.py
trufflepig/py.typed
trufflepig/rare_inference.py
trufflepig/reasoning.py
trufflepig/reference.py
trufflepig/reporting.py
trufflepig/rna_qc.py
trufflepig/sample_context.py
trufflepig/sample_quality.py
trufflepig/signal_views.py
trufflepig/subtype_signature.py
trufflepig/tcga_decompose.py
trufflepig/therapeutic_agents.py
trufflepig/therapy_response.py
trufflepig/transcript_to_gene.py
trufflepig/tumor_evidence.py
trufflepig/tumor_purity.py
trufflepig/tumor_type_ontology.py
trufflepig/version.py
trufflepig/workspace.py
trufflepig/analyze/__init__.py
trufflepig/analyze/cancer_type_context.py
trufflepig/analyze/comparison.py
trufflepig/analyze/deltas.py
trufflepig/analyze/flow.py
trufflepig/analyze/models.py
trufflepig/data/heme-tumor-up-vs-matched-normal.csv
trufflepig/data/subtype-deconvolved-expression.csv.gz
trufflepig/data/tcga-deconvolved-expression.csv.gz
trufflepig/data/therapeutic-agents.csv
trufflepig/data/therapeutic-targets.csv
trufflepig/data/tumor-up-vs-matched-normal.csv
trufflepig/decomposition/__init__.py
trufflepig/decomposition/engine.py
trufflepig/decomposition/panels.py
trufflepig/decomposition/plot.py
trufflepig/decomposition/signature.py
trufflepig/decomposition/subtype_refs.py
trufflepig/decomposition/templates.py
trufflepig/stages/__init__.py
trufflepig/web/__init__.py
trufflepig/web/app.py
trufflepig/web/runs.py
trufflepig/web/static/app.js
trufflepig/web/static/index.html
trufflepig/web/static/style.css