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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
- Summary Variant stats
- Sample stats
- Variant Cohort stats
- Family stats
- Distance matrixKnockout
- Population stratification (PCA)
- Identity-by-state (IBS) test
Population stratification - Principal component analysis (PCA)
Genome wide association studies (GWAS) - Fisher test Chi square test
- Family-based association analysis Transmission disequilibrium test (TDT)
Knockout Analysis
PCA
ExternalWrapper 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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