[r-client] cBioPortalData: Example Bioconductor Workflow #83
Description
Background:
The cBioPortal R client opens up cancer sequencing data hosted on the cBioPortal for Cancer Genomics to alternative analysis platforms such as Bioconductor, an open source software for bioinformatics built on R.
Bioconductor provides many workflows for demonstrating use-cases for particular packages, analyses, visualizations, and technologies including (but not limited to):
All of the available Bioconductor workflows may be found here: http://bioconductor.org/packages/release/BiocViews.html#___Workflow
The cBioPortal provides a REST API for programmatic access to the data and leverages this same service to generate the visualizations and reports seen throughout the site. Although the types of visualizations and reports already available and provided by the cBioPortal are extensive, one may require additional customization options for their specific needs that cannot yet be done through the cBioPortal itself. Connecting to the API directly allows anyone to build their own custom visualizations and reports to suit their needs.
Users may access the REST API through command line tools, such as curl, or through API clients. The cBioPortal team has made 2 such API clients available: one written in R and another written in python. More information on these API clients and how to access and use them can be found here.
R is one of the leading programming languages in Data Science. As such, building an example Bioconductor workflow demonstrating the use of the cBioPortalData R client will be greatly beneficial to the cancer research community as a whole by making analyses and visualization of cancer sequencing data even more accessible.
Goal:
To create an example Bioconductor workflow and iPython notebook demonstrating the use of cBioPortalData R client and a general Bioconductor approach to data analysis. To write supporting functions for visualizing and parsing metadata from the cBioPortalData endpoints as provided in the MultiAssayExperiment object obtained from cBioPortalData.
Approach:
- Provide a template workflow using cBioPortalData á la Bioconductor Workflows (package)
- Implement exploratory visualizations using MultiAssayExperiment (e.g., from
trackViewer) - Incorportate metadata from cBioPortalData effectively using Bioconductor data classes
Needed skills:
- Some basic knowledge of working with web services
R(analysis and pkg dev), Bioconductor