bio-workflows-multi-omics-pipeline - Multi-omics integration pipeline
Integrates transcriptomics, proteomics, and metabolomics using MOFA2, mixOmics, and SNF for downstream interpretation.
Tags
Updated: 2026-09-24Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Harmonize samples across modalities
- Select variable features per modality
- Train MOFA2 multi-omics models
- Perform mixOmics DIABLO integration
- Fuse similarity networks with SNF
- Interpret factors and feature weights
- Perform GO enrichment analysis
- Conduct survival analysis on factors
Inputs
- RNA-seq normalized count files
- Proteomics normalized data files
- Metabolomics normalized data files
- Sample metadata files
Outputs
- Trained MOFA model files
- Visualization plot files
- CSV factor values and weights
Requirements
- R environment
- MOFA2 package
- mixOmics package
- SNFtool package
- clusterProfiler package
- survival package