HiPiler

An interactive web application for exploring and visualizing regions-of-interest in large genome interaction matrices.

Introduction

HiPiler is an interactive web application for exploring and visualizing many regions-of-interest in large genome interaction matrices. Genome interaction matrices approximate the physical distance of pairs of genomic regions to each other and can contain up to 3 million rows and columns. Traditional matrix aggregation or pan-and-zoom interfaces largely fail in supporting search, inspection, and comparison of local regions-of-interest. HiPiler represents regions-of-interest as thumbnail-like snippets. Snippets can be laid out automatically based on their data and meta attributes. They are linked back to the matrix and can be explored interactively.

Get Started

Live demo: http://hipiler.higlass.io

Video introduction: https://youtu.be/qoLqje5OYKg

Project information: http://hipiler.lekschas.de

User documentation: http://hipiler.higlass.io/docs

Development

Dependencies

npm run update

Commands

npm start          // Start dev server
npm run build      // Build JS bundles
npm run build-app  // Build entire app
npm run update     // Update to latest code

Config

For custom settings copy config.json...

cp config.json config.local.json

...and adjust config.local.json to your liking.

Dynamic changes of the config are not supported yet. The dev server needs to be resarted to inline the new configuration.

Browser Support

HiPiler supports the latest version of Chrome and Firefox. Althought, almost everything works in Safari, t-SNE based clustering is broken. Once we fixed the bug Safari will be supported as well.

Note: Firefox by default starts searching on a website as soon as you start typing something. Unfortunately, this feature intereferes with keyboard shortcuts and can't be disabled with JS. If you want to use keyboard shortcuts in Firefox go to Tools > Options > Advanced > General Tab and disable Search for text when I start typing.