NetworkDataCompanion

NetworkDataCompanion provides functions to manage and preprocess TCGA and GTEx datasets and to support regulatory network inference with NetZoo from multi-omics data (RNA-seq, methylation) for cancer-focused regulatory network analyses.

Key Features:

• Integration with NetZoo: Integrates with NetZoo tools to infer regulatory network models from multi-omics data such as RNA-seq and methylation profiles.
• Reproducibility and Workflow Automation: Operates within the Nextflow workflow tcga-data-nf to download, preprocess, and analyze TCGA datasets, facilitating reproducible analyses.
• Data Management and Processing: Provides functions for managing, mapping, and filtering TCGA data to handle large-scale dataset preprocessing and organization.
• Application in Cancer Research: Supports analysis of cancer subtypes, including colon cancer, and exploration of differences potentially attributable to epigenetic mechanisms, and supplies pre-processed networks for the 10 most common cancer types.
• Flexibility and Extensibility: Offers a framework that can be adapted and integrated with other bioinformatics workflows for custom network inference and analysis.

Scientific Applications:

• Regulatory network analysis: Enables inference and analysis of gene and protein regulatory networks from TCGA and GTEx multi-omics data.
• Multi-omics integration: Supports integration of RNA-seq and methylation data into coherent network analyses.
• Method development and validation: Facilitates development and validation of computational methods for network inference using large cancer cohorts.
• Cancer subtype investigation: Applied to study cancer subtypes (e.g., colon cancer) and to investigate epigenetic contributions to subtype-specific network differences.

Methodology:

Integration with NetZoo for regulatory network inference from RNA-seq and methylation; inclusion in the Nextflow tcga-data-nf workflow for downloading, preprocessing, and analyzing TCGA datasets; functions for managing, mapping, and filtering TCGA data; generation of pre-processed networks for the 10 most common cancer types.