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hipiler

Visual exploration of large genome interaction matrices with interactive small multiples.

https://github.com/flekschas/hipiler

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.3%) to scientific vocabulary

Keywords

3d-genome chromosome-conformation-capture genomics hi-c small-multiples visualization
Last synced: 4 months ago · JSON representation ·

Repository

Visual exploration of large genome interaction matrices with interactive small multiples.

Basic Info
  • Host: GitHub
  • Owner: flekschas
  • License: mit
  • Language: JavaScript
  • Default Branch: master
  • Homepage: http://hipiler.higlass.io
  • Size: 11.9 MB
Statistics
  • Stars: 13
  • Watchers: 4
  • Forks: 0
  • Open Issues: 12
  • Releases: 19
Topics
3d-genome chromosome-conformation-capture genomics hi-c small-multiples visualization
Created about 9 years ago · Last pushed about 4 years ago
Metadata Files
Readme Changelog License Citation

README.md

HiPiler

HiPiler's interface

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

Build Status Demo Video doi

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

bash npm run update

Commands

JavaScript 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.

Owner

  • Name: Fritz Lekschas
  • Login: flekschas
  • Kind: user
  • Location: Somerville, MA

Computer scientist researching visualization systems for large-scale exploration of biomedical data. Harvard CS PhD '21.

Citation (CITATION.bib) 

@article{lekschas2018hipiler,
  author = {Fritz Lekschas and Benjamin Bach and Peter Kerpedjiev and Nils Gehlenborg and Hanspeter Pfister},
  title = {HiPiler: Visual Exploration Of Large Genome Interaction Matrices With Interactive Small Multiples},
  journal = {IEEE Transactions on Visualization and Computer Graphics},
  series = {InfoVis ’17},
  year = {2018},
  month = {1},
  day = {1},
  volume = {24},
  number = {1},
  pages = {522-531},
  doi = {10.1109/TVCG.2017.2745978},
}

GitHub Events

Total
Last Year

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 29
  • Total pull requests: 1
  • Average time to close issues: 4 months
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 0.76
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • flekschas (27)
  • liz-is (1)
Pull Request Authors
  • dependabot[bot] (1)
Top Labels
Issue Labels
feature (15) enhancement (10) bug (3) question (1)
Pull Request Labels
dependencies (1)

Dependencies

package-lock.json npm
  • 1400 dependencies
package.json npm
  • aurelia-cli 0.35.1 development
  • aurelia-testing 1.0.0-beta.4.0.0 development
  • aurelia-tools 2.0.0 development
  • aurelia-validation 1.1.3 development
  • babel-core 6.26.3 development
  • babel-eslint 8.2.3 development
  • babel-plugin-syntax-flow 6.18.0 development
  • babel-plugin-transform-decorators-legacy 1.3.4 development
  • babel-plugin-transform-es2015-modules-amd 6.24.1 development
  • babel-plugin-transform-es2015-modules-commonjs 6.26.2 development
  • babel-plugin-transform-flow-strip-types 6.22.0 development
  • babel-polyfill 6.26.0 development
  • babel-preset-env 1.6.1 development
  • babel-preset-stage-1 6.24.1 development
  • babel-register 6.26.0 development
  • browser-sync 2.24.4 development
  • connect-history-api-fallback 1.5.0 development
  • eslint 4.19.1 development
  • eslint-config-airbnb 16.1.0 development
  • eslint-plugin-import 2.11.0 development
  • eslint-plugin-jsx-a11y 6.0.3 development
  • eslint-plugin-react 7.7.0 development
  • gulp github:gulpjs/gulp#4.0 development
  • gulp-babel 7.0.0 development
  • gulp-changed-in-place 2.3.0 development
  • gulp-clean 0.4.0 development
  • gulp-concat 2.6.1 development
  • gulp-eslint 4.0.2 development
  • gulp-htmlmin 4.0.0 development
  • gulp-if 2.0.2 development
  • gulp-modify 0.1.1 development
  • gulp-notify 3.2.0 development
  • gulp-order 1.1.1 development
  • gulp-plumber 1.2.0 development
  • gulp-rename 1.2.2 development
  • gulp-sass 4.0.1 development
  • gulp-sourcemaps 2.6.4 development
  • gulp-wrap 0.13.0 development
  • html-minifier 3.5.15 development
  • jasmine-core 2.8.0 development
  • karma 1.7.0 development
  • karma-babel-preprocessor 6.0.1 development
  • karma-chrome-launcher 2.2.0 development
  • karma-jasmine 1.1.0 development
  • merge-stream 1.0.1 development
  • minimatch 3.0.4 development
  • redux-freeze 0.1.5 development
  • through2 2.0.3 development
  • uglify-js 3.4.0 development
  • vinyl-fs 2.4.4 development
  • aurelia-animator-css 1.0.4
  • aurelia-bootstrapper 2.2.0
  • bluebird 3.5.1
  • chroma-js 1.3.7
  • d3 4.13.0
  • gulp-marked flekschas/gulp-marked
  • higlass 1.7.2
  • hull.js 0.2.10
  • javascript-detect-element-resize 0.5.3
  • localforage 1.7.1
  • marked 0.3.19
  • normalize-wheel 1.0.1
  • papaparse 4.4.0
  • pixi.js 5.2.0
  • react 16.6.3
  • react-bootstrap 0.32.1
  • react-dom 16.6.3
  • redux 3.7.2
  • redux-batched-actions 0.3.0
  • redux-persist 4.10.2
  • redux-thunk 2.2.0
  • redux-undo 1.0.0-beta9-9-7
  • requirejs 2.3.5
  • tayden-clusterfck 0.7.0
  • text github:requirejs/text#latest
  • three 0.92.0
  • three-line-2d 1.1.6
  • three-orbit-controls 82.1.0
  • tsne-js 1.0.3