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enhancer-gene-vis

A tool for visualizing ABC enhancer-gene connections in the context of genetic variants.

https://github.com/flekschas/enhancer-gene-vis

Science Score: 54.0%

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    CITATION.cff file
    Found CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    Found .zenodo.json file
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    Links to: nature.com
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    Scientific vocabulary similarity
    Low similarity (6.9%) to scientific vocabulary

Keywords

enhancer-gene enhancers variants visualization
Last synced: 6 months ago · JSON representation ·

Repository

A tool for visualizing ABC enhancer-gene connections in the context of genetic variants.

Basic Info
Statistics
  • Stars: 12
  • Watchers: 2
  • Forks: 4
  • Open Issues: 7
  • Releases: 0
Topics
enhancer-gene enhancers variants visualization
Created over 5 years ago · Last pushed almost 3 years ago
Metadata Files
Readme License Citation

README.md

ABC Enhancer-Gene Visualization

**A tool for visually exploring ABC enhancer-gene connections across biosamples in the context of genetic variants**


![User Interface](https://user-images.githubusercontent.com/932103/108857083-b40b3e00-75b8-11eb-88aa-0ff00c4bb8bc.png)

Website: https://flekschas.github.io/enhancer-gene-vis

Paper: Nasser et al., "Genome-wide enhancer maps link risk variants to disease genes", Nature, 2021.

This web-based visualization provides access to genome-wide ABC enhancer-gene connections across 131 biosamples and allows you to correlated the enhancers with genetic variants.

How?

Coming Soon! Meanwhile please read the introduction.

Development

Setting up a development environment

Installation

bash $ git clone https://github.com/flekschas/enhancer-gene-vis && enhancer-gene-vis $ npm install

Commands

Developmental server: npm start Production build: npm run build Demo build: npm run build-demo

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{nasser2021genome,
  title = {Genome-wide enhancer maps link disease variants to genes and cell types},
  author = {Joseph Nasser and Drew T. Bergman and Charles P. Fulco and Philine Guckelberger and Benjamin R. Doughty and Tejal A. Patwardhan and Thouis R. Jones and Tung H. Nguyen and Jacob C. Ulirsch and Fritz Lekschas and Kristy Mualim and Heini M. Natri and Elle M. Weeks and Glen Munson and Michael Kane and Helen Y. Kang and Ang Cui and John P. Ray and Thomas M. Eisenhaure and Ryan L. Collins and Kushal Dey and Hanspeter Pfister and Alkes L. Price and Charles B. Epstein and Anshul Kundaje and Ramnik J. Xavier and Mark J. Daly and Hailiang Huang and Hilary K. Finucane and Nir Hacohen and Eric S. Lander and Jesse M. Engreitz},
  journal = {Nature},
  year = {2021},
  month = {4},
  day = {7},
  url = {https://doi.org/10.1038/s41586-021-03446-x},
  doi = {10.1038/s41586-021-03446-x},
}

GitHub Events

Total
Last Year

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 7
  • Total pull requests: 64
  • Average time to close issues: about 12 hours
  • Average time to close pull requests: 4 days
  • Total issue authors: 4
  • Total pull request authors: 2
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.16
  • Merged pull requests: 52
  • Bot issues: 0
  • Bot pull requests: 12
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
  • kailashbp (2)
  • flekschas (2)
  • zhilongjia (2)
  • AGunnell77 (1)
Pull Request Authors
  • riyavsinha (52)
  • dependabot[bot] (12)
Top Labels
Issue Labels
enhancement (3) bug (2) question (1)
Pull Request Labels
dependencies (12)

Dependencies

package-lock.json npm
  • 1694 dependencies
package.json npm
  • eslint-config-airbnb ^18.2.0 development
  • eslint-config-prettier ^6.11.0 development
  • eslint-plugin-prettier ^3.1.4 development
  • gh-pages ^3.1.0 development
  • prettier ^2.0.5 development
  • @flatten-js/interval-tree ^1.0.13
  • @flekschas/utils ^0.25.0
  • @material-ui/core ^4.11.0
  • @material-ui/icons ^4.9.1
  • @material-ui/lab ^4.0.0-alpha.56
  • @testing-library/jest-dom ^4.2.4
  • @testing-library/react ^9.5.0
  • @testing-library/user-event ^7.2.1
  • d3 ^6.2.0
  • higlass ^1.11.3
  • higlass-arcs ^0.3.0
  • higlass-register ^0.3.0
  • lodash-es ^4.17.15
  • pixi.js ^5.3.0
  • prop-types ^15.7.2
  • pub-sub-es ^1.2.2
  • query-string ^6.13.1
  • react ^16.13.1
  • react-bootstrap 0.32.1
  • react-dom ^16.13.1
  • react-scripts 3.4.1
  • recoil ^0.1.2
  • tinyqueue ^2.0.3
environment.yml conda
  • cytoolz
  • nodejs >=12
  • pip
  • pysam
  • python >=3.7