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This is under active development at the moment, it will implemented in next version 2.0.0 |
Analysis
There are several native variant analysis implemented in OpenCGA, these use internal the different internal APIs developed to provide a scalable and high-performance implementation. Occasionally, these analysis can store results in the variant storage to allow users to filter by them, for instance GWAS analysis can be stored and/or indexed for filtering.
The analysis available include:
- Basic statistics Stats
- Sample Stats
- GWAS
- ...
- stats
- Sample stats
- Cohort stats
- Family stats
- Knockout
- Population stratification (PCA)
- Identity-by-state (IBS)
- Genome wide association studies (GWAS)
- Family-based association analysis (TDT)
Knockout Analysis
PCA
Wrapper Analysis
You can use external tools using the wrapper analysis. Some tools are being implemented naively and available to all users.
- Plink
- rv-tests
Customisation
Users can easily extend and customise OpenCGA for their analysis.
Table of Contents:
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