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)