These are the instruction to reproduce the results of the paper called “Multi-omic analysis unveils biological pathways in peripheral immune system associated to minimal hepatic encephalopathy appearance in cirrhotic patients”

Teresa Rubio, Vicente Felipo, Sonia Tarazona, Roberta Pastorelli, Desamparados Escudero-García, Joan Tosca, Amparo Urios, Ana Conesa, Carmina Montoliu.

Scripts

- **01_SingleOmicsAnalsis**: 
  - transcriptomics (R script for differential expression + enrichment analysis): output + R script
  - metabolomics (R script for differential expression analysis): output + R script
  - cytokines (R script for differential expression analysis): output + R script

- **02_Multi-Omics_Integration**:
  - 01_clustering (output of metabolites and cytokines clustering analysis)
  - 02_performance (output of PLS analysis and model performance)
  - 03_enrichment_analysis (output of mdgsa analysis with genes ranked by PLS loadings)
  - MultiOmicsAnalysis_script.R (R script to produce the 3 above outputs)
  
- **revision**: scripts to answer reviewers questions

- **all_sparse_functions.R** (R script with homemade PLS additional functions)

- **auxiliary_functions.R** (R script with homemade auxiliary functions)