RNA Expression Web Based Visualization

[skeenan]

Background

RNA expression data associates genomic features that gives a perspective into the genetic activity within a cell medium. Experiments often relate sample and expression data to discover how a drug or environmental context can affect gene expression.

The GA4GH API has recently integrated RNA expression data models, which makes it possible to quickly and easily analyze and visualize a rich genomics data type over HTTP. This opens up genomics to a wide world of visualization tools that can be developed against a unified interface.

Major tasks

• Access RNA expression data made available over a GA4GH API via a Web browser.
• Integrate or develop a heatmap visualization that displays expression data for multiple samples.
• Create a minimal interface for discovering and selecting data to visualize.

  Ideal candidates

Some familiarity with client-side programming is required. Basic knowledge of interacting with HTTP servers via JavaScript will make it easier to understand how the application gathers data. To effectively implement a visualization some experience with an existing visualization method would be helpful, for example D3.js or R-Shiny.

Note: a server providing RNA expression data will be made available for hack-a-thon participants.

[hitz]

Where is the API spec for RNA expression datamodels?

[skeenan]

@kozbo can answer

[kozbo]

@hitz see the RNA schema files here: https://github.com/ga4gh/schemas/tree/master/src/main/proto/ga4gh We should have an RNA API server up by Oct 10.