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https://github.com/broadinstitute/genetic-prevalence-estimator

https://github.com/broadinstitute/genetic-prevalence-estimator

Science Score: 36.0%

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
  • ✓
    Committers with academic emails
    2 of 4 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.1%) to scientific vocabulary

Keywords from Contributors

genomics
Last synced: 10 months ago · JSON representation

Repository

Basic Info
Statistics
  • Stars: 4
  • Watchers: 2
  • Forks: 0
  • Open Issues: 51
  • Releases: 0
Created about 5 years ago · Last pushed 12 months ago
Metadata Files
Readme Contributing License

README.md

Genetic Prevalence Estimator, GeniE

![Frontend CI status badge](https://github.com/broadinstitute/genetic-prevalence-estimator/actions/workflows/frontend-ci.yml/badge.svg) ![Backend CI status badge](https://github.com/broadinstitute/genetic-prevalence-estimator/actions/workflows/website-ci.yml/badge.svg)

The prevalence GeniE tool aims to estimate carrier frequency and genetic prevalence for recessive conditions using allele frequencies from population data in gnomAD. We provide support for creating variant lists from ClinVar and gnomAD, or allow users to build their own custom list using gnomAD IDs.

Website

https://genie.broadinstitute.org/

Development

See CONTRIBUTING.md.

Owner

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

Broad Institute of MIT and Harvard

GitHub Events

Total
  • Issues event: 31
  • Watch event: 3
  • Delete event: 16
  • Issue comment event: 14
  • Push event: 79
  • Pull request review comment event: 14
  • Pull request review event: 18
  • Pull request event: 41
  • Create event: 19
Last Year
  • Issues event: 31
  • Watch event: 3
  • Delete event: 16
  • Issue comment event: 14
  • Push event: 79
  • Pull request review comment event: 14
  • Pull request review event: 18
  • Pull request event: 41
  • Create event: 19

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 620
  • Total Committers: 4
  • Avg Commits per committer: 155.0
  • Development Distribution Score (DDS): 0.411
Past Year
  • Commits: 61
  • Committers: 2
  • Avg Commits per committer: 30.5
  • Development Distribution Score (DDS): 0.197
Top Committers
Name Email Commits
Nick Watts n****s@b****g 365
Riley Grant g****h@g****m 242
Elissa Alarmani e****n@b****g 12
Josephine Lee 5****4 1
Committer Domains (Top 20 + Academic)
broadinstitute.org: 2

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 122
  • Total pull requests: 27
  • Average time to close issues: 3 months
  • Average time to close pull requests: 24 days
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 0.64
  • Average comments per pull request: 0.15
  • Merged pull requests: 19
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 18
  • Pull requests: 27
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 24 days
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.15
  • Merged pull requests: 19
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • nawatts (85)
  • sambaxter (35)
  • rileyhgrant (22)
  • elissa-alarmani (3)
  • aymanm (1)
Pull Request Authors
  • rileyhgrant (26)
  • elissa-alarmani (17)
  • josephinelee1234 (1)
  • sambaxter (1)
Top Labels
Issue Labels
Component: frontend (63) Component: worker (32) Component: website (31) Component: data pipelines (26) High priority (11) Component: infrastructure (7) Component: documentation (4) Bug (4) Resolution: wontfix (2) Priority: High (2) Resolution: duplicate (1) Epic (1)
Pull Request Labels
Bug (1) High priority (1) Component: frontend (1) good first issue (1)

Dependencies

.github/workflows/frontend-ci.yml actions
  • actions/checkout v2 composite
  • actions/setup-node v1 composite
.github/workflows/pipeline-ci.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/website-ci.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
docker-compose.yml docker
  • gcr.io/google.com/cloudsdktool/cloud-sdk latest
  • postgres 13.1
frontend/package-lock.json npm
  • 1648 dependencies
frontend/package.json npm
  • @types/react-window ^1.8.8 development
  • fishery ^2.2.2 development
  • http-proxy-middleware ^1.3.1 development
  • prettier 2.2.1 development
  • @chakra-ui/icons ^1.0.13
  • @chakra-ui/react ^1.6.1
  • @emotion/react ^11.4.0
  • @emotion/styled ^11.3.0
  • @gnomad/identifiers ^2.3.0
  • @testing-library/jest-dom ^5.11.4
  • @testing-library/react ^11.1.0
  • @testing-library/user-event ^12.1.10
  • @types/jest ^26.0.15
  • @types/lodash ^4.14.169
  • @types/node ^12.0.0
  • @types/qs ^6.9.6
  • @types/react ^17.0.0
  • @types/react-dom ^17.0.0
  • @types/react-router-dom ^5.1.7
  • @visx/axis ^2.1.0
  • @visx/group ^2.1.0
  • @visx/legend ^2.1.0
  • @visx/scale ^2.1.0
  • @visx/shape ^2.1.0
  • d3-interpolate ^3.0.1
  • downshift ^6.1.7
  • framer-motion ^4.1.16
  • lodash ^4.17.21
  • qs ^6.10.1
  • react ^17.0.2
  • react-dom ^17.0.2
  • react-router-dom ^5.2.0
  • react-scripts 4.0.3
  • react-window ^1.8.10
  • typescript ^4.1.2
calculator/setup.py pypi
data-pipelines/requirements-pipeline.in pypi
  • beautifulsoup4 *
  • hail ==0.2.120
  • numpy <1.26.0
  • pandas *
data-pipelines/requirements-pipeline.txt pypi
  • aiodns ==2.0.0
  • aiohttp ==3.9.5
  • aiosignal ==1.3.1
  • async-timeout ==4.0.3
  • asyncinit ==0.2.4
  • attrs ==23.2.0
  • avro ==1.11.3
  • azure-common ==1.1.28
  • azure-core ==1.30.1
  • azure-identity ==1.16.0
  • azure-mgmt-core ==1.4.0
  • azure-mgmt-storage ==20.1.0
  • azure-storage-blob ==12.20.0
  • beautifulsoup4 ==4.12.3
  • bokeh ==3.4.1
  • boto3 ==1.34.106
  • botocore ==1.34.106
  • cachetools ==5.3.3
  • certifi ==2024.2.2
  • cffi ==1.16.0
  • charset-normalizer ==3.3.2
  • click ==8.1.7
  • commonmark ==0.9.1
  • contourpy ==1.2.1
  • cryptography ==42.0.7
  • decorator ==4.4.2
  • deprecated ==1.2.14
  • dill ==0.3.8
  • frozenlist ==1.4.1
  • google-api-core ==2.19.0
  • google-auth ==2.29.0
  • google-cloud-core ==2.4.1
  • google-cloud-storage ==2.16.0
  • google-crc32c ==1.5.0
  • google-resumable-media ==2.7.0
  • googleapis-common-protos ==1.63.0
  • hail ==0.2.120
  • humanize ==1.1.0
  • hurry-filesize ==0.9
  • idna ==3.7
  • isodate ==0.6.1
  • janus ==1.0.0
  • jinja2 ==3.1.4
  • jmespath ==1.0.1
  • jproperties ==2.1.1
  • markupsafe ==2.1.5
  • msal ==1.28.0
  • msal-extensions ==1.1.0
  • msrest ==0.7.1
  • multidict ==6.0.5
  • nest-asyncio ==1.6.0
  • numpy ==1.25.2
  • oauthlib ==3.2.2
  • orjson ==3.10.3
  • packaging ==24.0
  • pandas ==2.2.2
  • parsimonious ==0.10.0
  • pillow ==10.3.0
  • plotly ==5.22.0
  • portalocker ==2.8.2
  • proto-plus ==1.23.0
  • protobuf ==3.20.2
  • py4j ==0.10.9.5
  • pyasn1 ==0.6.0
  • pyasn1-modules ==0.4.0
  • pycares ==4.4.0
  • pycparser ==2.22
  • pygments ==2.18.0
  • pyjwt ==2.8.0
  • pyspark ==3.3.4
  • python-dateutil ==2.9.0.post0
  • python-json-logger ==2.0.7
  • pytz ==2024.1
  • pyyaml ==6.0.1
  • regex ==2024.5.15
  • requests ==2.31.0
  • requests-oauthlib ==2.0.0
  • rich ==12.6.0
  • rsa ==4.9
  • s3transfer ==0.10.1
  • scipy ==1.9.3
  • shellingham ==1.5.4
  • six ==1.16.0
  • sortedcontainers ==2.4.0
  • soupsieve ==2.5
  • tabulate ==0.9.0
  • tenacity ==8.3.0
  • tornado ==6.4
  • typer ==0.12.3
  • typing-extensions ==4.11.0
  • tzdata ==2024.1
  • urllib3 ==1.26.18
  • uvloop ==0.19.0
  • wrapt ==1.16.0
  • xyzservices ==2024.4.0
  • yarl ==1.9.4
dev-requirements.in pypi
  • black * development
  • nox * development
  • pip-tools * development
  • pre-commit * development
  • pylint * development
  • pylint-django * development
  • pytest * development
  • pytest-cov * development
  • pytest-django * development
  • wheel * development
dev-requirements.txt pypi
  • argcomplete ==3.2.1 development
  • astroid ==3.0.2 development
  • black ==23.12.1 development
  • build ==1.0.3 development
  • cfgv ==3.4.0 development
  • click ==8.1.7 development
  • colorlog ==6.8.0 development
  • coverage ==7.4.0 development
  • dill ==0.3.7 development
  • distlib ==0.3.8 development
  • exceptiongroup ==1.2.0 development
  • filelock ==3.13.1 development
  • identify ==2.5.33 development
  • importlib-metadata ==7.0.1 development
  • iniconfig ==2.0.0 development
  • isort ==5.13.2 development
  • mccabe ==0.7.0 development
  • mypy-extensions ==1.0.0 development
  • nodeenv ==1.8.0 development
  • nox ==2023.4.22 development
  • packaging ==23.2 development
  • pathspec ==0.12.1 development
  • pip-tools ==7.3.0 development
  • platformdirs ==4.1.0 development
  • pluggy ==1.3.0 development
  • pre-commit ==3.6.0 development
  • pylint ==3.0.3 development
  • pylint-django ==2.5.5 development
  • pylint-plugin-utils ==0.8.2 development
  • pyproject-hooks ==1.0.0 development
  • pytest ==7.4.4 development
  • pytest-cov ==4.1.0 development
  • pytest-django ==4.7.0 development
  • pyyaml ==6.0.1 development
  • tomli ==2.0.1 development
  • tomlkit ==0.12.3 development
  • typing-extensions ==4.9.0 development
  • virtualenv ==20.25.0 development
  • wheel ==0.42.0 development
  • zipp ==3.17.0 development
pyproject.toml pypi
shared-requirements.in pypi
  • Django *
  • djangorestframework *
  • rules *
shared-requirements.txt pypi
  • asgiref ==3.3.4
  • django ==3.2
  • djangorestframework ==3.12.4
  • pytz ==2021.1
  • rules ==3.0
  • sqlparse ==0.4.1
website/setup.py pypi
website/website-requirements.in pypi
  • google-auth *
  • google-cloud-pubsub *
  • whitenoise *
website/website-requirements.txt pypi
  • cachetools ==5.3.2
  • certifi ==2023.11.17
  • charset-normalizer ==3.3.2
  • google-api-core ==2.15.0
  • google-auth ==2.26.2
  • google-cloud-pubsub ==2.19.0
  • googleapis-common-protos ==1.62.0
  • grpc-google-iam-v1 ==0.13.0
  • grpcio ==1.60.0
  • grpcio-status ==1.60.0
  • idna ==3.6
  • proto-plus ==1.23.0
  • protobuf ==4.25.2
  • pyasn1 ==0.5.1
  • pyasn1-modules ==0.3.0
  • requests ==2.31.0
  • rsa ==4.9
  • urllib3 ==2.1.0
  • whitenoise ==6.6.0
worker/setup.py pypi
worker/worker-requirements.in pypi
  • hail *
  • requests *
worker/worker-requirements.txt pypi
  • aiodns ==2.0.0
  • aiohttp ==3.9.1
  • aiosignal ==1.3.1
  • async-timeout ==4.0.3
  • asyncinit ==0.2.4
  • attrs ==23.1.0
  • avro ==1.11.3
  • azure-common ==1.1.28
  • azure-core ==1.29.5
  • azure-identity ==1.15.0
  • azure-mgmt-core ==1.4.0
  • azure-mgmt-storage ==20.1.0
  • azure-storage-blob ==12.19.0
  • bokeh ==3.3.1
  • boto3 ==1.29.7
  • botocore ==1.32.7
  • cachetools ==5.3.2
  • certifi ==2023.11.17
  • cffi ==1.16.0
  • charset-normalizer ==3.3.2
  • click ==8.1.7
  • commonmark ==0.9.1
  • contourpy ==1.2.0
  • cryptography ==41.0.5
  • decorator ==4.4.2
  • deprecated ==1.2.14
  • dill ==0.3.7
  • frozenlist ==1.4.0
  • google-api-core ==2.14.0
  • google-auth ==2.23.4
  • google-cloud-core ==2.3.3
  • google-cloud-storage ==2.13.0
  • google-crc32c ==1.5.0
  • google-resumable-media ==2.6.0
  • googleapis-common-protos ==1.61.0
  • hail ==0.2.120
  • humanize ==1.1.0
  • hurry-filesize ==0.9
  • idna ==3.6
  • isodate ==0.6.1
  • janus ==1.0.0
  • jinja2 ==3.1.2
  • jmespath ==1.0.1
  • jproperties ==2.1.1
  • markupsafe ==2.1.3
  • msal ==1.25.0
  • msal-extensions ==1.0.0
  • msrest ==0.7.1
  • multidict ==6.0.4
  • nest-asyncio ==1.5.8
  • numpy ==1.25.2
  • oauthlib ==3.2.2
  • orjson ==3.9.10
  • packaging ==23.2
  • pandas ==2.1.3
  • parsimonious ==0.10.0
  • pillow ==10.1.0
  • plotly ==5.18.0
  • portalocker ==2.8.2
  • protobuf ==3.20.2
  • py4j ==0.10.9.5
  • pyasn1 ==0.5.1
  • pyasn1-modules ==0.3.0
  • pycares ==4.4.0
  • pycparser ==2.21
  • pygments ==2.17.2
  • pyjwt ==2.8.0
  • pyspark ==3.3.3
  • python-dateutil ==2.8.2
  • python-json-logger ==2.0.7
  • pytz ==2023.3.post1
  • pyyaml ==6.0.1
  • regex ==2023.10.3
  • requests ==2.31.0
  • requests-oauthlib ==1.3.1
  • rich ==12.6.0
  • rsa ==4.9
  • s3transfer ==0.8.0
  • scipy ==1.9.3
  • six ==1.16.0
  • sortedcontainers ==2.4.0
  • tabulate ==0.9.0
  • tenacity ==8.2.3
  • tornado ==6.3.3
  • typer ==0.9.0
  • typing-extensions ==4.8.0
  • tzdata ==2023.3
  • urllib3 ==1.26.18
  • uvloop ==0.19.0
  • wrapt ==1.16.0
  • xyzservices ==2023.10.1
  • yarl ==1.9.3