There and Back Again: A Multi-Omics Tale of Thyroid Co-Expression Network Rewiring – Supplementary Materials

This dataset provides supplementary materials, including data, code, and intermediate results required to reproduce the analyses presented in the manuscript: "There and Back Again: A Multi-Omics Tale of Thyroid Co-Expression Network Rewiring" Contents include:- Preprocessed multi-omics input datasets used for WGCNA network construction, along with associated data (annotations and trait correlations) (data_input_multiomics_WGCNA.zip) - R Markdown workflows for all analysis steps (Rmd_workflows_multiomics_WGCNA.zip)- Over-representation analysis results (ORA_results_multiomics_WGCNA.zip)- Supplementary material (Pozhidaeva_et_al_Supplementary_material.pdf) The workflows cover: - Comparison of the correlation structure of the data across different preprocessing methods (00_Comparison_correlation_structure.Rmd; 00_Comparison_correlation_structure.bib)- Network construction (01_network_construction.Rmd)- Module–trait association analysis (02_module_trait.Rmd)- Module preservation analysis across pairwise comparisons (03_1_module_preservation_control_treated.Rmd, 03_2_module_preservation_treated_recovery.Rmd, 03_3_module_preservation_control_recovery.Rmd)- Pathway enrichment analysis for all modules (04_ORA_all_networks.Rmd)- Differential connectivity analysis across pairwise comparisons (05_1_DiffK_control_treated.Rmd, 05_2_DiffK_treated_recovery.Rmd, 05_3_DiffK_control_recovery.Rmd, calc_pvalues_diffK.R) A containerized computational environment is provided to ensure full reproducibility.The container includes all required R packages and dependencies and can be executed using Singularity:singularity exec multiomics_WGCNA.sif R