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Open Source Science

https://github.com/broadinstitute/variant-curation-portal

Web application for curating loss of function variants

https://github.com/broadinstitute/variant-curation-portal

Science Score: 26.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Web application for curating loss of function variants

Basic Info
Statistics
  • Stars: 4
  • Watchers: 5
  • Forks: 1
  • Open Issues: 48
  • Releases: 0
Created over 7 years ago · Last pushed 12 months ago
Metadata Files
Readme Contributing License

README.md

Variant Curation Portal

![Frontend CI status badge](https://github.com/broadinstitute/variant-curation-portal/actions/workflows/frontend-ci.yml/badge.svg) ![Backend CI status badge](https://github.com/broadinstitute/variant-curation-portal/actions/workflows/backend-ci.yml/badge.svg)

Development

See CONTRIBUTING.md.

Creating a project on the portal

  • Navigate to https://lof.curation.broadinstitute.org/projects.

  • Click "Create project", name the project (often this is the gene symbol, e.g. 'PCSK9')

  • Create a list of variants using the script

    • For a single gene python scripts/get_gnomad_lof_variants.py --gene-ids ENSG00000169174 --gnomad-version 4 --output ./data/PCSK9.json
    • For a list of variants python scripts/get_gnomad_lof_variants.py --gnomad-version 4 --variants-file ./data/input_variants.csv --output ./data/output_variants.json

  • Navigate back to the portal, on the project click "Upload variants"

  • Upload the list of variants generated by the script

  • Add the emails of the project leads(s) as additional project owners

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

GitHub Events

Total
  • Issues event: 3
  • Member event: 1
  • Push event: 5
  • Pull request event: 2
  • Create event: 1
Last Year
  • Issues event: 3
  • Member event: 1
  • Push event: 5
  • Pull request event: 2
  • Create event: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 45
  • Total pull requests: 57
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 1 day
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 0.51
  • Average comments per pull request: 0.21
  • Merged pull requests: 57
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 1
  • Average time to close issues: 19 days
  • Average time to close pull requests: 19 days
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • nawatts (44)
  • rileyhgrant (3)
  • msingerb (2)
  • phildarnowsky-broad (1)
  • carmenglaze1 (1)
Pull Request Authors
  • nawatts (56)
  • dependabot[bot] (28)
  • rileyhgrant (7)
Top Labels
Issue Labels
Type: Bug (7) Area: Admin (6) Area: Curation (4) Resolution: Won't Fix (2) Area: Data Import (2) Area: Documentation (1) Area: Search (1)
Pull Request Labels
dependencies (28) javascript (22) python (6)

Dependencies

package.json npm
  • @babel/core ^7.10.5 development
  • @babel/plugin-proposal-class-properties ^7.10.4 development
  • @babel/plugin-transform-runtime ^7.10.5 development
  • @babel/preset-env ^7.10.4 development
  • @babel/preset-react ^7.10.4 development
  • @testing-library/react ^10.0.1 development
  • babel-eslint ^10 development
  • babel-loader ^8.1.0 development
  • clean-webpack-plugin ^3.0.0 development
  • copy-webpack-plugin ^5.1.1 development
  • css-loader ^3.4.1 development
  • eslint ^6.8.0 development
  • eslint-config-airbnb 18.1.0 development
  • eslint-config-prettier 6.10.0 development
  • eslint-plugin-import ^2 development
  • eslint-plugin-jsx-a11y ^6 development
  • eslint-plugin-prettier ^3 development
  • eslint-plugin-react ^7 development
  • eslint-plugin-react-hooks ^2.5.0 development
  • file-loader ^5.0.2 development
  • jest ^25.1.0 development
  • mini-css-extract-plugin ^0.9.0 development
  • prettier ^1.19.1 development
  • style-loader ^1.1.2 development
  • webpack ^4.41.5 development
  • webpack-bundle-tracker ^0.4.3 development
  • webpack-cli ^3.3.10 development
  • webpack-dev-server ^3.10.1 development
  • core-js ^3.0.0
  • lodash ^4.17
  • mousetrap ^1.6
  • prop-types ^15.7
  • query-string 5
  • react ^16.8
  • react-dom ^16.8
  • react-redux ^7.1.0
  • react-router-dom ^5.0.0
  • redux ^4.0.4
  • redux-thunk ^2.3.0
  • semantic-ui-css ^2.4.1
  • semantic-ui-react ^0.86.0
yarn.lock npm
  • 1109 dependencies
requirements-dev.txt pypi
  • black ==19.3b0 development
  • pip-tools ==4.4.1 development
  • pydocstyle ==3.0.0 development
  • pylint ==2.4.4 development
  • pylint-django ==2.0.14 development
  • pytest ==4.3.1 development
  • pytest-cov ==2.7.1 development
  • pytest-django ==3.4.8 development
  • tox ==3.7.0 development
requirements.in pypi
  • Django *
  • django-filter *
  • django-webpack-loader *
  • djangorestframework *
  • rules *
  • whitenoise *
requirements.txt pypi
  • django ==2.2.24
  • django-filter ==2.2.0
  • django-webpack-loader ==0.6.0
  • djangorestframework ==3.11.2
  • pytz ==2019.1
  • rules ==2.0.1
  • sqlparse ==0.3.0
  • whitenoise ==4.1.2
Dockerfile docker
  • node lts-alpine build
  • python 3.6-alpine build
docker/docker-compose-base.yml docker
  • postgres 9.6-alpine
docker/nginx-basic-auth/docker-compose.yml docker
  • nginx stable-alpine
docker/oauth-proxy/docker-compose.yml docker
  • quay.io/oauth2-proxy/oauth2-proxy v6.0.0
docker/docker-compose-dev.yml docker
pyproject.toml pypi
.github/workflows/backend-ci.yml actions
  • actions/cache v1 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/frontend-ci.yml actions
  • actions/cache v1 composite
  • actions/checkout v2 composite
  • actions/setup-node v1 composite