This repository contains code for the RatGTEx web portal, which provides gene expression and eQTL data for different rat tissues.

There are also repositories for the RatGTEx data pipeline and to process those results for this site's API and visualizations.

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Using Jekyll to build the site

This site uses Jekyll to build the pages for each genome version.

Using Rollup to bundle the visualization scripts

Rollup installation

To install Rollup and required libraries, you may run npm install in this directory. This will install the libraries under a subdirectory: node_modules.

Rollup configuration

The rollup configuration files for each visualization is located in the directory src/rollup. To recompile the code for a particular visualization, run the following command in this directory:

rollup -c src/rollup/rollup.expression-map.config.js

This will recompile and generate a new bundled visualization script in the directory assets/js/.

Dependencies

RatGTEx Visualizations is distributed, in part, under and subject to the provisions of licenses for:

D3.js (https://d3js.org/), Copyright (c) 2017 Mike Bostock. All rights reserved. Licensed under the BSD 3-clause license (https://opensource.org/licenses/BSD-3-Clause); and

jQuery (https://jquery.com/), Copyright (c) 2018 The jQuery Foundation. All rights reserved. Licensed under the MIT license (https://jquery.org/license/).

Acknowledgements

Visualization code was adapted from the GTEx portal visualizations.