CHANGELOG.md
CITATION.cff
CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE
MANIFEST.in
PYPI_RELEASE_CHECKLIST.md
README.md
RELEASE_CHECKLIST.md
codemeta.json
environment.yml
pyproject.toml
configs/templates/external_validation.yaml
configs/templates/mathys_csv.yaml
configs/templates/mps_model.yaml
configs/templates/sea_ad_minimal.yaml
configs/templates/target_gene_panel.yaml
docs/apple_silicon_mps.md
docs/benchmarking_and_validation.md
docs/cli_reference.md
docs/external_validation_expansion.md
docs/input_formats.md
docs/input_output_schema.md
docs/installation.md
docs/interpretation_guide.md
docs/license_and_data_use.md
docs/limitations.md
docs/pnas_validation_strategy.md
docs/pypi_release.md
docs/quickstart.md
docs/real_world_geo_smoke_test_gse20141.md
docs/reproducibility.md
docs/reproducible_commands.md
docs/research_use_only.md
docs/reviewer_guidance.md
docs/runtime_benchmarks.md
docs/troubleshooting.md
docs/tutorial_mathys_external_validation.md
docs/tutorial_neurofate_axis.md
docs/tutorial_sea_ad.md
examples/format_examples/ensembl_ids/README.md
examples/format_examples/ensembl_ids/expected_outputs_summary.tsv
examples/format_examples/ensembl_ids/expression.tsv
examples/format_examples/ensembl_ids/metadata.tsv
examples/format_examples/genes_by_samples/README.md
examples/format_examples/genes_by_samples/expected_outputs_summary.tsv
examples/format_examples/genes_by_samples/expression.tsv
examples/format_examples/genes_by_samples/metadata.tsv
examples/format_examples/long_format/README.md
examples/format_examples/long_format/expected_outputs_summary.tsv
examples/format_examples/long_format/expression.tsv
examples/format_examples/long_format/metadata.tsv
examples/format_examples/microarray_probe_map/README.md
examples/format_examples/microarray_probe_map/expected_outputs_summary.tsv
examples/format_examples/microarray_probe_map/expression.tsv
examples/format_examples/microarray_probe_map/metadata.tsv
examples/format_examples/microarray_probe_map/probe_map.tsv
examples/format_examples/samples_by_genes/README.md
examples/format_examples/samples_by_genes/expected_outputs_summary.tsv
examples/format_examples/samples_by_genes/expression.csv
examples/format_examples/samples_by_genes/metadata.csv
examples/tiny_demo/tiny_expected_output_summary.tsv
examples/tiny_demo/tiny_gene_panel.tsv
examples/tiny_demo/tiny_metadata.tsv
examples/tiny_demo/tiny_sparse_expression.tsv
examples/tiny_demo/tiny_sparse_expression.tsv.gz
metadata/dataset_intake_checklist.tsv
metadata/dataset_registry.tsv
metadata/dataset_selection_plan.tsv
metadata/external_validation_registry.tsv
metadata/feature_registry.tsv
metadata/manuscript_module_map.tsv
metadata/minimum_viable_dataset_plan.tsv
metadata/neurofate_axis_endpoint_registry.tsv
metadata/neurofate_axis_gene_aliases.tsv
metadata/neurofate_axis_registry.tsv
metadata/phase15_external_validation_candidates.tsv
metadata/phase23_replication_cohort_registry.tsv
metadata/phase28_ad_replication_registry.tsv
metadata/phase33_pd_replication_registry.tsv
metadata/phase34_pd_replication_registry.tsv
metadata/provenance_template.tsv
metadata/real_dataset_sources.tsv
metadata/target_gene_panel_v1.tsv
metadata/checksums/gse243639_sha256.tsv
neurofate/__init__.py
neurofate/__main__.py
neurofate/adapters.py
neurofate/axis.py
neurofate/benchmarking.py
neurofate/cli.py
neurofate/demo.py
neurofate/evolution.py
neurofate/features.py
neurofate/graph.py
neurofate/ingest.py
neurofate/io.py
neurofate/microbiome.py
neurofate/models.py
neurofate/qc.py
neurofate/reports.py
neurofate/singlecell.py
neurofate.egg-info/PKG-INFO
neurofate.egg-info/SOURCES.txt
neurofate.egg-info/dependency_links.txt
neurofate.egg-info/entry_points.txt
neurofate.egg-info/requires.txt
neurofate.egg-info/top_level.txt
neurofate/resources/__init__.py
neurofate/resources/neurofate_axis_gene_aliases.tsv
neurofate/resources/neurofate_axis_registry.tsv
neurofate/resources/tiny_demo/__init__.py
neurofate/resources/tiny_demo/tiny_gene_panel.tsv
neurofate/resources/tiny_demo/tiny_metadata.tsv
neurofate/resources/tiny_demo/tiny_sparse_expression.tsv
tests/test_bioinformatics_full_methods_manuscript.py
tests/test_bioinformatics_manuscript_claims.py
tests/test_cli.py
tests/test_cli_help.py
tests/test_cli_public_commands.py
tests/test_config.py
tests/test_dataset_intake_checklist.py
tests/test_dataset_registry.py
tests/test_dataset_selection_plan.py
tests/test_docs_exist.py
tests/test_endpoint_adapter.py
tests/test_feature_registry.py
tests/test_imports.py
tests/test_ingest_expression_metadata_join.py
tests/test_ingest_format_detection.py
tests/test_ingest_gene_identifier_mapping.py
tests/test_ingest_geo_series_matrix.py
tests/test_ingest_metadata_inference.py
tests/test_ingest_orientation_detection.py
tests/test_intake_config.py
tests/test_manual_download_templates.py
tests/test_manuscript_module_map.py
tests/test_mathys_metadata_safety.py
tests/test_mathys_sparse_safety.py
tests/test_neurofate_run_end_to_end.py
tests/test_no_overclaiming_audit.py
tests/test_output_inventory.py
tests/test_phase12_benchmark_config.py
tests/test_phase12_evidence_strength.py
tests/test_phase12_leakage_audit.py
tests/test_phase12_no_label_features.py
tests/test_phase13_claim_strength.py
tests/test_phase13_mathys_audit.py
tests/test_phase13_no_overclaiming.py
tests/test_phase13_package_builders.py
tests/test_phase14_release_completeness.py
tests/test_phase15_cli.py
tests/test_phase15_dataset_registry.py
tests/test_phase15_external_file_inspector.py
tests/test_phase15_extraction_planner.py
tests/test_phase15_metadata_mapping.py
tests/test_phase15_validation_reliability.py
tests/test_phase16_gse243639_extractor_safety.py
tests/test_phase16_gse243639_feature_table.py
tests/test_phase16_gse243639_metadata_parser.py
tests/test_phase16_gse243639_validation_claims.py
tests/test_phase17_celltype_feature_table.py
tests/test_phase17_no_overclaiming.py
tests/test_phase17_pd_validation_safety.py
tests/test_phase17_umap_annotation_inspector.py
tests/test_phase18_annotation_repair.py
tests/test_phase18_cell_id_matching.py
tests/test_phase18_feature_count.py
tests/test_phase18_no_overclaiming.py
tests/test_phase19_cell_id_forensics.py
tests/test_phase19_linkage_decision.py
tests/test_phase19_no_forced_annotation.py
tests/test_phase19_row_order_safety.py
tests/test_phase20_feature_builder_safe_map.py
tests/test_phase20_no_overclaiming.py
tests/test_phase20_safe_map_schema.py
tests/test_phase20_validation_safety.py
tests/test_phase21_axis_claims.py
tests/test_phase21_axis_registry.py
tests/test_phase21_axis_scores.py
tests/test_phase21_evidence_consolidation.py
tests/test_phase21_no_overclaiming.py
tests/test_phase21_random_controls.py
tests/test_phase22_claim_strength.py
tests/test_phase22_endpoint_locked_associations.py
tests/test_phase22_endpoint_registry.py
tests/test_phase22_no_overclaiming.py
tests/test_phase22_random_controls_endpoint_locked.py
tests/test_phase23_axis_matrix_builder.py
tests/test_phase23_manual_download_guards.py
tests/test_phase23_no_overclaiming.py
tests/test_phase23_replication_claims.py
tests/test_phase23_replication_registry.py
tests/test_phase24_extraction_planner.py
tests/test_phase24_gse184950_metadata_parser.py
tests/test_phase24_no_fastq_processing.py
tests/test_phase24_no_overclaiming.py
tests/test_phase24_raw_archive_lister.py
tests/test_phase25_archive_reconciliation.py
tests/test_phase25_gse184950_endpoint.py
tests/test_phase25_no_fastq_processing.py
tests/test_phase25_selective_extraction_plan.py
tests/test_phase25_series_matrix_parser.py
tests/test_phase26_axis_extractor_sparse.py
tests/test_phase26_nested_archive_inspector.py
tests/test_phase26_no_fastq_processing.py
tests/test_phase26_replication_claims.py
tests/test_phase26_selective_extractor_safety.py
tests/test_phase27_clean_axis_scores.py
tests/test_phase27_gse184950_sample_integrity.py
tests/test_phase27_no_overclaiming.py
tests/test_phase27_pnas_readiness_matrix.py
tests/test_phase27_replication_evidence_logic.py
tests/test_phase28_ad_replication_claims.py
tests/test_phase28_ad_replication_registry.py
tests/test_phase28_axis_matrix_builder.py
tests/test_phase28_geo_series_parser.py
tests/test_phase28_no_overclaiming.py
tests/test_phase29_ad_replication_endpoint.py
tests/test_phase29_bulk_axis_converter.py
tests/test_phase29_no_overclaiming.py
tests/test_phase29_rda_inspector.py
tests/test_phase29_replication_claims.py
tests/test_phase30_gse174367_ad_endpoint.py
tests/test_phase30_gse174367_axis_conversion.py
tests/test_phase30_gse174367_sample_mapping.py
tests/test_phase30_no_overclaiming.py
tests/test_phase31_axis_gene_aliases.py
tests/test_phase31_converter_gene_mapping.py
tests/test_phase31_gse174367_gene_id_audit.py
tests/test_phase31_no_overclaiming.py
tests/test_phase32_claim_language.py
tests/test_phase32_crosscohort_evidence_summary.py
tests/test_phase32_no_overclaiming.py
tests/test_phase32_pnas_readiness.py
tests/test_phase33_geo_series_axis_extractor.py
tests/test_phase33_no_overclaiming.py
tests/test_phase33_pd_replication_claims.py
tests/test_phase33_pd_replication_registry.py
tests/test_phase33_platform_mapping.py
tests/test_phase34_geo_metadata_parser.py
tests/test_phase34_no_overclaiming.py
tests/test_phase34_pd_replication_claims.py
tests/test_phase34_pd_replication_registry.py
tests/test_phase34_platform_probe_mapping.py
tests/test_phase35_geo_expression_join.py
tests/test_phase35_gse20141_sample_mapping.py
tests/test_phase35_no_overclaiming.py
tests/test_phase35_pd_axis_score_builder.py
tests/test_phase36_builder_metadata_debug.py
tests/test_phase36_gse20141_label_consumption.py
tests/test_phase36_no_overclaiming.py
tests/test_phase36_pd_axis_score_builder.py
tests/test_phase37_gse7621_metadata.py
tests/test_phase37_gse7621_sample_mapping.py
tests/test_phase37_no_overclaiming.py
tests/test_phase37_pd_axis_replication_logic.py
tests/test_phase38_gse7621_direction_audit.py
tests/test_phase38_no_overclaiming.py
tests/test_phase38_pd_divergence_classification.py
tests/test_phase38_pnas_readiness.py
tests/test_phase39_elife_readiness.py
tests/test_phase39_no_overclaiming.py
tests/test_phase39_publication_claims.py
tests/test_phase3_figure_generation.py
tests/test_phase3_sparse_statistics_safety.py
tests/test_phase4_figures.py
tests/test_phase4_statistics_safety.py
tests/test_phase5_feature_table.py
tests/test_phase5_model_safety.py
tests/test_phase6_model_config.py
tests/test_phase6_mps_safety.py
tests/test_phase7_crosscohort_safety.py
tests/test_phase7_harmonization.py
tests/test_phase9_mathys_csv_safety.py
tests/test_phase9_mathys_feature_alignment.py
tests/test_provenance_template.py
tests/test_provenance_validator.py
tests/test_public_cli_reports.py
tests/test_pypi_packaging.py
tests/test_real_dataset_sources.py
tests/test_release_artifact_separation.py
tests/test_release_demo_and_ingest.py
tests/test_release_metadata.py
tests/test_release_packaging_metadata.py
tests/test_release_public_cli.py
tests/test_release_readme_manual.py
tests/test_release_research_use_only.py
tests/test_report_generation_safety.py
tests/test_reproducibility_manifest.py
tests/test_research_use_only_language.py
tests/test_research_use_only_outputs.py
tests/test_run_demo_end_to_end.py
tests/test_safety_flags.py
tests/test_sea_ad_category_decoder_safety.py
tests/test_sea_ad_metadata_extractor_safety.py
tests/test_sea_ad_metadata_summary_script.py
tests/test_sparse_gene_extraction_safety.py
tests/test_target_gene_panel.py
tests/test_tiny_demo.py