multiomics_integration

Overview

This repository contains the scripts used for the integration of miRNA, proteomics, and metabolomics data to investigate disease subclassification and biological insights in patients with Primary Sclerosing Cholangitis (PSC).

The workflow includes data preprocessing, exploratory analyses, network-based approaches (WGCNA), and multi-omics integration using mixOmics.

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Repository Structure

1️⃣ Data preprocessing

These scripts load the raw .csv files and perform preprocessing steps to prepare each omics layer and the associated metadata for downstream analyses and multi-omics integration.

• metadata_preprocessing.R
• miRNA_preprocessing.R
• protein_preprocessing.R
• metabolite_preprocessing.R

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2️⃣ Data analysis and integration

The following R Markdown files perform exploratory analyses, network analysis, and multi-omics integration.

• data_exploration.Rmd
• WGCNA_multi_omics.Rmd
• mixOmics_multi_omics.Rmd

Important note The files suffixed with _vf.Rmd (e.g. data_exploration_vf.Rmd, WGCNA_multi_omics_vf.Rmd, mixOmics_multi_omics_vf.Rmd) correspond to the corrected and final versions used for the results reported in the associated manuscript. The non-_vf versions represent earlier versions prior to final corrections and refinements.

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3️⃣ Additional / legacy scripts

These scripts are provided for completeness and reproducibility but are not used in the final analyses presented in the manuscript.

• WGCNA_conc.Rmd Older version of the multi-omics WGCNA approach using concatenated data.

• WGCNA_uniomic.Rmd WGCNA performed separately on each omics layer without concatenation or integration.

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Reproducibility

All analyses were performed in R. Package versions, parameters, and methodological details are documented within each script or R Markdown file to ensure reproducibility.

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Authors and Affiliation

Ghada Nouairia Annika Bergquist Group Center for Bioinformatics and Biostatistics Department of Medicine, Huddinge (MedH) Karolinska Institutet, Sweden