Introduction
The paper introduces SmCCNet 2.0, an advanced tool for the integration of multi-omics data with a focus on phenotype-specific network analysis. Leveraging Sparse multiple canonical correlation network analysis (SmCCNet), this second-generation tool adeptly handles both single and multiple omics data types alongside quantitative or binary phenotypes. It enhances the practical utility by offering a streamlined, flexible setup and automates the entire pipeline, significantly boosting user-friendliness and computational efficiency. Key features include automated data preprocessing, robust network analysis with hierarchical clustering, subnetwork pruning, and an innovative RShiny application for detailed network visualization.
Overview
This repository hosts all the essential components used and presented in the manuscript of SmCCNet 2.0. It includes:
- Subnetwork Results (Subnetworks folder): All subnetwork results (.Rdata metadata, network visualization, and more) discussed in the manuscript are stored here for reference and further analysis, all results are run based on SmCCNet 2.0.1.
- Source Code of the Shiny Application (ShinyApp folder): The complete source code for the RShiny application used for network visualization is available, allowing users to explore and modify the visualization tool.
- Source Package (Package folder): The full R package for SmCCNet 2.0.1, which includes functions for network analysis, data preprocessing, and integration of multi-omics data.
- TCGA Breast Cancer Data (Data folder): The dataset used in the examples provided in the manuscript, is available in CSV format, enabling users to replicate the study results or conduct their analyses.
Additional Resources and Contact Information
For more detailed information about the SmCCNet package, including its functionalities, installation instructions, and usage examples, please visit the following links:
If you have any questions regarding the tool or need further assistance, feel free to contact Dr. Katerina Kechris at [katerina.kechris@cuanschutz.edu](mailto: Dr. Katerina.Kechris.