FileName,Category,Description,Source,FileSizeBytes
README.md,documentation,Deposit documentation and interpretation boundaries,,~
ENVIRONMENT.md,documentation,Computational environment and software versions,,~
FILE_INVENTORY.csv,documentation,Complete file listing with descriptions (this file),,~
.zenodo.json,metadata,Zenodo metadata record (JSON),,~
data/derived/DE_miRNA_85_unique.csv,derived,S1 Table: 85 unique DE-miRNAs with expression statistics,See output_manifest.csv,~
data/derived/candidate_validated_aging_72_genes.csv,derived,S2 Table: 72-gene candidate validated-aging analysis set,See output_manifest.csv,~
data/derived/Hallmark_all50_C_layer.csv,derived,S3 Table: All-50 Hallmark Fisher test statistics,See output_manifest.csv,~
data/derived/Hallmark_all50_no_miR4454.csv,derived,S4 Table: Hallmark statistics without miR-4454-only genes,See output_manifest.csv,~
data/derived/Hallmark_miR4454_comparison.csv,derived,S5 Table: Hallmark miR-4454 sensitivity comparison,See output_manifest.csv,~
data/derived/STRING_input_audit.csv,derived,S6 Table: STRING PPI input-only audit,See output_manifest.csv,~
data/derived/STRING_node_degrees.csv,derived,S7 Table: Corrected input-only STRING node degrees,See output_manifest.csv,~
data/derived/STRING_edge_list.csv,derived,S8 Table: Corrected input-only STRING edge list,See output_manifest.csv,~
data/derived/GO_BP_redundancy_groups.csv,derived,S9 Table: GO BP gene-overlap redundancy groups,See output_manifest.csv,~
data/derived/GO_miR4454_sensitivity.csv,derived,S10 Table: GO hsa-miR-4454 gene-retention sensitivity,See output_manifest.csv,~
data/derived/miR4454_C_layer_membership.csv,derived,S11 Table: hsa-miR-4454 C-layer gene membership sensitivity,See output_manifest.csv,~
data/derived/label_sensitivity_Welch.csv,derived,S12 Table: Exhaustive ordinary-Welch results (56 labelings),See output_manifest.csv,~
data/derived/label_sensitivity_summary.csv,derived,S13 Table: Label-sensitivity summary statistics,See output_manifest.csv,~
data/derived/PCA_coordinates.csv,derived,S14 Table: Regenerated PCA coordinates and variance,See output_manifest.csv,~
data/derived/candidate_selection_audit.csv,derived,S15 Table: Candidate-selection audit table,See output_manifest.csv,~
data/source/README.md,documentation,Instructions for downloading source data from public databases,,~
figures/source_data/Fig1_source_data.csv,figure_source,Volcano plot and heatmap source data,Derived from S1 Table,~
figures/source_data/Fig2_source_data.csv,figure_source,miRNA-target network source data,Derived from S2 Table,~
figures/source_data/Fig3_source_data.csv,figure_source,GO/KEGG enrichment source data,Derived from S3/S9/S10 Tables,~
figures/source_data/Fig4_source_data.csv,figure_source,STRING PPI source data,Derived from S7 Table,~
figures/source_data/S1_S6_source_data.csv,figure_source,Supplementary figure source data index,Cross-reference to derived tables,~
figures/source_data/Table1_source_data.csv,figure_source,Table 1 GO BP terms source data,Derived from GO BP enrichment,~
scripts/R/01_preprocess_normalize.R,script,R script: Human miRNA filtering + quantile normalisation + PCA,,~
scripts/R/02_differential_expression.R,script,R script: limma DE analysis,,~
scripts/R/03_enrichment_analysis.R,script,R script: GO BP / Hallmark / KEGG enrichment,,~
scripts/R/04_label_sensitivity.R,script,R script: Exhaustive label-sensitivity enumeration,,~
scripts/python/01_label_sensitivity_audit.py,script,Python script: Welch t-test enumeration (56 labelings),,~
scripts/python/02_string_ppi_audit.py,script,Python script: STRING export processing and audit,,~
scripts/python/03_candidate_selection_audit.py,script,Python script: Candidate-selection rule audit,,~
scripts/python/04_consistency_checks.py,script,Python script: Manuscript-supplement consistency checks,,~
manifests/input_manifest.csv,manifest,Input file manifest with versions and access dates,,~
manifests/output_manifest.csv,manifest,Output file manifest with provenance chain,,~