D3b CBTN Summit Workshop

CBTN Multi-Omic Subtyping

This repo provides the necessary setup and analysis scripts to demonstrate the use of CBTN data for multi-omic clustering within the Cavatica Cloud Environment.

In this workshop, we will perform the following:

1. Open a new cloud-based RStudio instance within Cavatica's Data Studio
2. Clone the d3b-cbtn-summit github repository using the terminal within RStudio
3. Review the modules within the repository and their key functionality.
4. Prepare epigenomic, transcriptomic, and alternatively splice transcriptome data for high-grade astrocytomas (HGATs) as input to multi-omic clustering.
5. Run intNMF matrix factorization for multi-omic clustering using the three data layers outlined in (4).
6. Evaluate novel subtypes in relation to known disease subtypes and survival characteristics.
7. Evaluate cluster-specific differential expression patterns.
8. Time permitting, evaluate cluster-specific differential methylation and differentially methylated pathways.