file	configured_source	resolved_source	source_kind	status
nmd_vcell_database_resource_v0.5.0-20260716.tar.gz	results/nar_resource_pack/nmd_vcell_database_resource_v0.5.0-20260716.tar.gz	results/nar_resource_pack/nmd_vcell_database_resource_v0.5.0-20260716.tar.gz	configured_source	present
nmd_vcell_database_resource_v0.5.0-20260716.tar.gz.sha256	results/nar_resource_pack/nmd_vcell_database_resource_v0.5.0-20260716.tar.gz.sha256	results/nar_resource_pack/nmd_vcell_database_resource_v0.5.0-20260716.tar.gz.sha256	configured_source	present
nmd_vcell_release_manifest.tsv	results/nar_resource_pack/nmd_vcell_release_manifest.tsv	results/nar_resource_pack/nmd_vcell_release_manifest.tsv	configured_source	present
nmd_vcell_release_checksums.sha256	results/nar_resource_pack/nmd_vcell_release_checksums.sha256	results/nar_resource_pack/nmd_vcell_release_checksums.sha256	configured_source	present
nmd_vcell_data_dictionary_v0.5.0.tsv	results/nar_resource_pack/nmd_vcell_data_dictionary_v0.5.0.tsv	results/nar_resource_pack/nmd_vcell_data_dictionary_v0.5.0.tsv	configured_source	present
gpu_closure_handoff_20260710.tar.gz	results/gpu_strategy/gpu_closure_handoff_20260710.tar.gz	results/gpu_strategy/gpu_closure_handoff_20260710.tar.gz	configured_source	superseded_not_publicly_hosted
gpu_closure_handoff_20260710.tar.gz.sha256	results/gpu_strategy/gpu_closure_handoff_20260710.tar.gz.sha256	results/gpu_strategy/gpu_closure_handoff_20260710.tar.gz.sha256	configured_source	superseded_not_publicly_hosted
final_gpu_closure_manifest_20260710.tsv	results/gpu_strategy/final_gpu_closure_manifest_20260710.tsv	results/gpu_strategy/final_gpu_closure_manifest_20260710.tsv	configured_source	present
feature_delta_head_comparison.tsv	results/state_nadig_trade_fewshot/delta_feature/feature_delta_head_comparison.tsv	public_resource/downloads/feature_delta_head_comparison.tsv	locked_v05_download	present
feature_delta_uncertainty_summary.tsv	results/high_quality_upgrade/statistical_audit/feature_delta_uncertainty_summary.tsv	public_resource/downloads/feature_delta_uncertainty_summary.tsv	locked_v05_download	present
feature_delta_paired_tests.tsv	results/high_quality_upgrade/statistical_audit/feature_delta_paired_tests.tsv	public_resource/downloads/feature_delta_paired_tests.tsv	locked_v05_download	present
feature_delta_strict_gate.tsv	results/high_quality_upgrade/statistical_audit/feature_delta_strict_gate.tsv	public_resource/downloads/feature_delta_strict_gate.tsv	locked_v05_download	present
external_context_uncertainty.tsv	results/high_quality_upgrade/statistical_audit/external_context_uncertainty.tsv	public_resource/downloads/external_context_uncertainty.tsv	locked_v05_download	present
PUBLICATION_GRADE_STATISTICAL_AUDIT.md	results/high_quality_upgrade/statistical_audit/PUBLICATION_GRADE_STATISTICAL_AUDIT.md	public_resource/downloads/PUBLICATION_GRADE_STATISTICAL_AUDIT.md	locked_v05_download	present
repeated_heldout_gene_summary.tsv	results/high_quality_upgrade/repeated_heldout_ridge/repeated_heldout_gene_summary.tsv	public_resource/downloads/repeated_heldout_gene_summary.tsv	locked_v05_download	present
repeated_heldout_gene_paired_tests.tsv	results/high_quality_upgrade/repeated_heldout_ridge/repeated_heldout_gene_paired_tests.tsv	public_resource/downloads/repeated_heldout_gene_paired_tests.tsv	locked_v05_download	present
repeated_heldout_gene_gates.tsv	results/high_quality_upgrade/repeated_heldout_ridge/repeated_heldout_gene_gates.tsv	public_resource/downloads/repeated_heldout_gene_gates.tsv	locked_v05_download	present
v2_vs_v1_feature_comparison.tsv	results/high_quality_upgrade/repeated_heldout_ridge/v2_vs_v1_feature_comparison.tsv	public_resource/downloads/v2_vs_v1_feature_comparison.tsv	locked_v05_download	present
REPEATED_HELDOUT_GENE_RIDGE_REPORT.md	results/high_quality_upgrade/repeated_heldout_ridge/REPEATED_HELDOUT_GENE_RIDGE_REPORT.md	public_resource/downloads/REPEATED_HELDOUT_GENE_RIDGE_REPORT.md	locked_v05_download	present
feature_ablation_cross_seed_summary.tsv	results/high_quality_upgrade/feature_ablation_leakage/feature_ablation_cross_seed_summary.tsv	public_resource/downloads/feature_ablation_cross_seed_summary.tsv	locked_v05_download	present
feature_ablation_gates.tsv	results/high_quality_upgrade/feature_ablation_leakage/feature_ablation_gates.tsv	public_resource/downloads/feature_ablation_gates.tsv	locked_v05_download	present
feature_ablation_vs_full_cross_seed.tsv	results/high_quality_upgrade/feature_ablation_leakage/feature_ablation_vs_full_cross_seed.tsv	public_resource/downloads/feature_ablation_vs_full_cross_seed.tsv	locked_v05_download	present
FEATURE_ABLATION_LEAKAGE_AUDIT_REPORT.md	results/high_quality_upgrade/feature_ablation_leakage/FEATURE_ABLATION_LEAKAGE_AUDIT_REPORT.md	public_resource/downloads/FEATURE_ABLATION_LEAKAGE_AUDIT_REPORT.md	locked_v05_download	present
gse293514_external_validation_summary.tsv	results/high_quality_upgrade/external_muscle_phenotype/gse293514_external_validation_summary.tsv	public_resource/downloads/gse293514_external_validation_summary.tsv	locked_v05_download	present
gse293514_external_validation_tests.tsv	results/high_quality_upgrade/external_muscle_phenotype/gse293514_external_validation_tests.tsv	public_resource/downloads/gse293514_external_validation_tests.tsv	locked_v05_download	present
gse293514_candidate_safety_flags.tsv	results/high_quality_upgrade/external_muscle_phenotype/gse293514_candidate_safety_flags.tsv	public_resource/downloads/gse293514_candidate_safety_flags.tsv	locked_v05_download	present
GSE293514_MUSCLE_FUSION_EXTERNAL_VALIDATION.md	results/high_quality_upgrade/external_muscle_phenotype/GSE293514_MUSCLE_FUSION_EXTERNAL_VALIDATION.md	public_resource/downloads/GSE293514_MUSCLE_FUSION_EXTERNAL_VALIDATION.md	locked_v05_download	present
linear_pca10_coverage.tsv	results/high_quality_upgrade/strong_baseline_panel/linear_pca10_coverage.tsv	public_resource/downloads/linear_pca10_coverage.tsv	locked_v05_download	present
linear_pca10_summary.tsv	results/high_quality_upgrade/strong_baseline_panel/linear_pca10_summary.tsv	public_resource/downloads/linear_pca10_summary.tsv	locked_v05_download	present
linear_pca10_paired_tests.tsv	results/high_quality_upgrade/strong_baseline_panel/linear_pca10_paired_tests.tsv	public_resource/downloads/linear_pca10_paired_tests.tsv	locked_v05_download	present
linear_pca10_gates.tsv	results/high_quality_upgrade/strong_baseline_panel/linear_pca10_gates.tsv	public_resource/downloads/linear_pca10_gates.tsv	locked_v05_download	present
linear_pca10_vs_ridge_v1.tsv	results/high_quality_upgrade/strong_baseline_panel/linear_pca10_vs_ridge_v1.tsv	public_resource/downloads/linear_pca10_vs_ridge_v1.tsv	locked_v05_download	present
NATURE_METHODS_LINEAR_BASELINE_REPORT.md	results/high_quality_upgrade/strong_baseline_panel/NATURE_METHODS_LINEAR_BASELINE_REPORT.md	public_resource/downloads/NATURE_METHODS_LINEAR_BASELINE_REPORT.md	locked_v05_download	present
gears_frozen_split_summary.tsv	results/high_quality_upgrade/official_baseline_gears/gears_frozen_split_summary.tsv	public_resource/downloads/gears_frozen_split_summary.tsv	locked_v05_download	present
gears_frozen_split_gates.tsv	results/high_quality_upgrade/official_baseline_gears/gears_frozen_split_gates.tsv	public_resource/downloads/gears_frozen_split_gates.tsv	locked_v05_download	present
gears_frozen_split_paired_tests.tsv	results/high_quality_upgrade/official_baseline_gears/gears_frozen_split_paired_tests.tsv	public_resource/downloads/gears_frozen_split_paired_tests.tsv	locked_v05_download	present
gears_vs_ridge_v1.tsv	results/high_quality_upgrade/official_baseline_gears/gears_vs_ridge_v1.tsv	public_resource/downloads/gears_vs_ridge_v1.tsv	locked_v05_download	present
gears_frozen_split_scores.tsv	results/high_quality_upgrade/official_baseline_gears/gears_frozen_split_scores.tsv	public_resource/downloads/gears_frozen_split_scores.tsv	locked_v05_download	present
gears_and_ridge_same_coverage_scores.tsv	results/high_quality_upgrade/official_baseline_gears/gears_and_ridge_same_coverage_scores.tsv	public_resource/downloads/gears_and_ridge_same_coverage_scores.tsv	locked_v05_download	present
GEARS_FROZEN_SPLIT_BENCHMARK_REPORT.md	results/high_quality_upgrade/official_baseline_gears/GEARS_FROZEN_SPLIT_BENCHMARK_REPORT.md	public_resource/downloads/GEARS_FROZEN_SPLIT_BENCHMARK_REPORT.md	locked_v05_download	present
scgpt_frozen_split_summary.tsv	results/high_quality_upgrade/official_baseline_scgpt/scgpt_frozen_split_summary.tsv	public_resource/downloads/scgpt_frozen_split_summary.tsv	locked_v05_download	present
scgpt_frozen_split_gates.tsv	results/high_quality_upgrade/official_baseline_scgpt/scgpt_frozen_split_gates.tsv	public_resource/downloads/scgpt_frozen_split_gates.tsv	locked_v05_download	present
scgpt_frozen_split_paired_tests.tsv	results/high_quality_upgrade/official_baseline_scgpt/scgpt_frozen_split_paired_tests.tsv	public_resource/downloads/scgpt_frozen_split_paired_tests.tsv	locked_v05_download	present
scgpt_vs_ridge_v1.tsv	results/high_quality_upgrade/official_baseline_scgpt/scgpt_vs_ridge_v1.tsv	public_resource/downloads/scgpt_vs_ridge_v1.tsv	locked_v05_download	present
scgpt_frozen_split_scores.tsv	results/high_quality_upgrade/official_baseline_scgpt/scgpt_frozen_split_scores.tsv	public_resource/downloads/scgpt_frozen_split_scores.tsv	locked_v05_download	present
scgpt_and_ridge_same_coverage_scores.tsv	results/high_quality_upgrade/official_baseline_scgpt/scgpt_and_ridge_same_coverage_scores.tsv	public_resource/downloads/scgpt_and_ridge_same_coverage_scores.tsv	locked_v05_download	present
SCGPT_FROZEN_SPLIT_BENCHMARK_REPORT.md	results/high_quality_upgrade/official_baseline_scgpt/SCGPT_FROZEN_SPLIT_BENCHMARK_REPORT.md	public_resource/downloads/SCGPT_FROZEN_SPLIT_BENCHMARK_REPORT.md	locked_v05_download	present
hepg2_candidate_decision_matrix_feature_delta_mlp_v2_lco.tsv	results/decision_support/hepg2_candidate_decision_matrix_feature_delta_mlp_v2_lco.tsv	results/decision_support/hepg2_candidate_decision_matrix_feature_delta_mlp_v2_lco.tsv	configured_source	present
nar_public_resource_gap_matrix_20260710.tsv	results/nar_resource_pack/nar_public_resource_gap_matrix_20260710.tsv	results/nar_resource_pack/nar_public_resource_gap_matrix_20260710.tsv	configured_source	present
REVIEWER_CRITIQUE_UPGRADE_REPORT.md	results/reviewer_critique_upgrade_20260716/REVIEWER_CRITIQUE_UPGRADE_REPORT.md	results/reviewer_critique_upgrade_20260716/REVIEWER_CRITIQUE_UPGRADE_REPORT.md	configured_source	present
signature_summary.tsv	results/reviewer_critique_upgrade_20260716/signature_summary.tsv	results/reviewer_critique_upgrade_20260716/signature_summary.tsv	configured_source	present
source_pairwise_concordance.tsv	results/reviewer_critique_upgrade_20260716/source_pairwise_concordance.tsv	results/reviewer_critique_upgrade_20260716/source_pairwise_concordance.tsv	configured_source	present
candidate_signature_stability.tsv	results/reviewer_critique_upgrade_20260716/candidate_signature_stability.tsv	results/reviewer_critique_upgrade_20260716/candidate_signature_stability.tsv	configured_source	present
tier_multiverse_summary.tsv	results/reviewer_critique_upgrade_20260716/tier_multiverse_summary.tsv	results/reviewer_critique_upgrade_20260716/tier_multiverse_summary.tsv	configured_source	present
direct_head_endpoint_effects.tsv	results/reviewer_critique_upgrade_20260716/direct_head_endpoint_effects.tsv	results/reviewer_critique_upgrade_20260716/direct_head_endpoint_effects.tsv	configured_source	present
direct_head_design_sensitivity.tsv	results/reviewer_critique_upgrade_20260716/direct_head_design_sensitivity.tsv	results/reviewer_critique_upgrade_20260716/direct_head_design_sensitivity.tsv	configured_source	present
repeated_ridge_effect_sizes.tsv	results/reviewer_critique_upgrade_20260716/repeated_ridge_effect_sizes.tsv	results/reviewer_critique_upgrade_20260716/repeated_ridge_effect_sizes.tsv	configured_source	present
muscle_target_coverage.tsv	results/reviewer_critique_upgrade_20260716/muscle_target_coverage.tsv	results/reviewer_critique_upgrade_20260716/muscle_target_coverage.tsv	configured_source	present
muscle_context_summary.tsv	results/reviewer_critique_upgrade_20260716/muscle_context_summary.tsv	results/reviewer_critique_upgrade_20260716/muscle_context_summary.tsv	configured_source	present
gtex_v8_muscle_target_coverage.tsv	results/reviewer_critique_upgrade_20260716/gtex_v8_muscle_target_coverage.tsv	results/reviewer_critique_upgrade_20260716/gtex_v8_muscle_target_coverage.tsv	configured_source	present
gtex_v8_muscle_target_expression_detail.tsv	results/reviewer_critique_upgrade_20260716/gtex_v8_muscle_target_expression_detail.tsv	results/reviewer_critique_upgrade_20260716/gtex_v8_muscle_target_expression_detail.tsv	configured_source	present
gtex_v8_source_metadata.tsv	results/reviewer_critique_upgrade_20260716/gtex_v8_source_metadata.tsv	results/reviewer_critique_upgrade_20260716/gtex_v8_source_metadata.tsv	configured_source	present
point_estimate_audit_long.tsv	results/reviewer_critique_upgrade_20260716/point_estimate_audit_long.tsv	results/reviewer_critique_upgrade_20260716/point_estimate_audit_long.tsv	configured_source	present
point_estimate_audit_summary.tsv	results/reviewer_critique_upgrade_20260716/point_estimate_audit_summary.tsv	results/reviewer_critique_upgrade_20260716/point_estimate_audit_summary.tsv	configured_source	present
nmd_support_score_components.tsv	results/reviewer_critique_upgrade_20260716/nmd_support_score_components.tsv	results/reviewer_critique_upgrade_20260716/nmd_support_score_components.tsv	configured_source	present
MAJOR_REVISION_RETROSPECTIVE_AUDIT.md	results/major_revision_20260716/MAJOR_REVISION_RETROSPECTIVE_AUDIT.md	results/major_revision_20260716/MAJOR_REVISION_RETROSPECTIVE_AUDIT.md	configured_source	present
NOISE_CEILING_REPORT.md	results/major_revision_20260716/NOISE_CEILING_REPORT.md	results/major_revision_20260716/NOISE_CEILING_REPORT.md	configured_source	present
repeated_split_pairwise_overlap.tsv	results/major_revision_20260716/repeated_split_pairwise_overlap.tsv	results/major_revision_20260716/repeated_split_pairwise_overlap.tsv	configured_source	present
repeated_split_gene_reuse.tsv	results/major_revision_20260716/repeated_split_gene_reuse.tsv	results/major_revision_20260716/repeated_split_gene_reuse.tsv	configured_source	present
noise_ceiling_cell_split_half.tsv	results/major_revision_20260716/noise_ceiling_cell_split_half.tsv	results/major_revision_20260716/noise_ceiling_cell_split_half.tsv	configured_source	present
noise_ceiling_batch_split.tsv	results/major_revision_20260716/noise_ceiling_batch_split.tsv	results/major_revision_20260716/noise_ceiling_batch_split.tsv	configured_source	present
noise_ceiling_guide_pair.tsv	results/major_revision_20260716/noise_ceiling_guide_pair.tsv	results/major_revision_20260716/noise_ceiling_guide_pair.tsv	configured_source	present
noise_ceiling_summary.tsv	results/major_revision_20260716/noise_ceiling_summary.tsv	results/major_revision_20260716/noise_ceiling_summary.tsv	configured_source	present
target_measurement_reliability.tsv	results/major_revision_20260716/target_measurement_reliability.tsv	results/major_revision_20260716/target_measurement_reliability.tsv	configured_source	present
dmd_source_specific_gene_effects.tsv	results/major_revision_20260716/dmd_source_specific_gene_effects.tsv	results/major_revision_20260716/dmd_source_specific_gene_effects.tsv	configured_source	present
dmd_multisource_evidence_modules.tsv	results/major_revision_20260716/dmd_multisource_evidence_modules.tsv	results/major_revision_20260716/dmd_multisource_evidence_modules.tsv	configured_source	present
dmd_multisource_evidence_module_counts.tsv	results/major_revision_20260716/dmd_multisource_evidence_module_counts.tsv	results/major_revision_20260716/dmd_multisource_evidence_module_counts.tsv	configured_source	present
dmd_signature2_meta_analysis_readiness.tsv	results/major_revision_20260716/dmd_signature2_meta_analysis_readiness.tsv	results/major_revision_20260716/dmd_signature2_meta_analysis_readiness.tsv	configured_source	present
depmap_26q1_leave_hepg2_out_provenance.json	results/major_revision_20260716/depmap_26q1_leave_hepg2_out_provenance.json	results/major_revision_20260716/depmap_26q1_leave_hepg2_out_provenance.json	configured_source	present
depmap_leave_hepg2_out_summary.tsv	results/major_revision_20260716/depmap_leave_hepg2_out_summary.tsv	results/major_revision_20260716/depmap_leave_hepg2_out_summary.tsv	configured_source	present
depmap_leave_hepg2_out_vs_released.tsv	results/major_revision_20260716/depmap_leave_hepg2_out_vs_released.tsv	results/major_revision_20260716/depmap_leave_hepg2_out_vs_released.tsv	configured_source	present
candidate_evidence_vector_v06.tsv	results/major_revision_20260716/candidate_evidence_vector_v06.tsv	results/major_revision_20260716/candidate_evidence_vector_v06.tsv	configured_source	present
34_major_revision_response_matrix_20260716.md	submission_nar_database/34_major_revision_response_matrix_20260716.md	submission_nar_database/34_major_revision_response_matrix_20260716.md	configured_source	present
35_claim_ladder_and_scientific_identity_20260716.md	submission_nar_database/35_claim_ladder_and_scientific_identity_20260716.md	submission_nar_database/35_claim_ladder_and_scientific_identity_20260716.md	configured_source	present
36_analysis_chronology_and_freeze_protocol_20260716.md	submission_nar_database/36_analysis_chronology_and_freeze_protocol_20260716.md	submission_nar_database/36_analysis_chronology_and_freeze_protocol_20260716.md	configured_source	present
37_feature_leakage_ledger.tsv	submission_nar_database/37_feature_leakage_ledger.tsv	submission_nar_database/37_feature_leakage_ledger.tsv	configured_source	present
38_model_cards_20260716.md	submission_nar_database/38_model_cards_20260716.md	submission_nar_database/38_model_cards_20260716.md	configured_source	present
39_resource_audit_comparison.tsv	submission_nar_database/39_resource_audit_comparison.tsv	submission_nar_database/39_resource_audit_comparison.tsv	configured_source	present
40_reproducibility_levels_manifest.tsv	submission_nar_database/40_reproducibility_levels_manifest.tsv	submission_nar_database/40_reproducibility_levels_manifest.tsv	configured_source	present
41_lockbox_noise_ceiling_protocol_20260716.md	submission_nar_database/41_lockbox_noise_ceiling_protocol_20260716.md	submission_nar_database/41_lockbox_noise_ceiling_protocol_20260716.md	configured_source	present
42_user_task_evaluation_protocol_20260716.md	submission_nar_database/42_user_task_evaluation_protocol_20260716.md	submission_nar_database/42_user_task_evaluation_protocol_20260716.md	configured_source	present