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aadamk committed Sep 18, 2024
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# D3b Bixu Repository Template
# D3b CBTN Summit Workshop

Use this template to bootstrap a new D3b bixu repository
### CBTN Multi-Omic Subtyping

### Badges
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.

Update the LICENSE badge to point to the new repo location on GitHub.
Note that the LICENSE badge will fail to render correctly unless the repo has
been set to **public**.
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.

Add additional badges for CI, docs, and other integrations as needed within the
`<p>` tag next to the LICENSE.

### Repo Description

Update the repositories description with a short summary of the repository's
intent.
Include an appropriate emoji at the start of the summary.

Add a handful of tags that summarize topics relating to the repository.
If the repo has a documentation site or webpage, add it next to the repository
description.

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