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genotype

Simple genotype comparison of VCF files

https://github.com/clinical-genomics/genotype

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
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.0%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Simple genotype comparison of VCF files

Basic Info
Statistics
  • Stars: 8
  • Watchers: 8
  • Forks: 2
  • Open Issues: 13
  • Releases: 10
Created almost 12 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Codeowners Authors

README.md

Genotype

Build Status - Github Coverage Status GitHub issues-closed Average time to resolve an issue Percentage of issues still open CodeFactor Code style: black Manage SNP calling comparisons at Clinical Genomics. The package exposes a CLI and a bare bones web interface to visualize results stored in a SQLite database.

Install

bash $ conda install -c bioconda pysam pyyaml sqlalchemy flask $ pip install genotype

Help?

Please check out the documentation

Owner

  • Name: Clinical Genomics
  • Login: Clinical-Genomics
  • Kind: organization
  • Location: Stockholm, Sweden

GitHub Events

Total
  • Create event: 1
Last Year
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 456
  • Total Committers: 14
  • Avg Commits per committer: 32.571
  • Development Distribution Score (DDS): 0.491
Past Year
  • Commits: 10
  • Committers: 3
  • Avg Commits per committer: 3.333
  • Development Distribution Score (DDS): 0.5
Top Committers
Name Email Commits
Robin Andeer r****r@g****m 232
Måns Magnusson m****n@s****e 72
Maya m****i@s****e 61
Patrik Grenfeldt p****t@s****e 56
Mropat m****t@g****m 13
Clinical Genomics Bot c****m@g****m 8
Henrik Stranneheim h****m@s****e 3
Kenny Billiau k****u@s****e 2
ChristianOertlin c****n@g****m 2
Barry Stokman 2****n 2
Kenny Billiau K****u@s****e 2
northwestwitch r****a@g****m 1
Maria Ropat 3****t 1
Robin Andeer r****r@s****e 1
Committer Domains (Top 20 + Academic)
scilifelab.se: 7

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 31
  • Total pull requests: 39
  • Average time to close issues: 8 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 9
  • Total pull request authors: 10
  • Average comments per issue: 0.81
  • Average comments per pull request: 1.87
  • Merged pull requests: 31
  • Bot issues: 0
  • Bot pull requests: 3
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • robinandeer (16)
  • moonso (7)
  • northwestwitch (2)
  • patrikgrenfeldt (1)
  • ChrOertlin (1)
  • SofiaOtero (1)
  • silvius76 (1)
  • Karl-Svard (1)
Pull Request Authors
  • henrikstranneheim (11)
  • patrikgrenfeldt (7)
  • mayabrandi (6)
  • moonso (5)
  • robinandeer (5)
  • dependabot[bot] (3)
  • ChrOertlin (2)
  • Mropat (2)
  • eliottBo (1)
  • northwestwitch (1)
Top Labels
Issue Labels
bug (3)
Pull Request Labels
dependencies (4) enhancement (1) bug (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 71 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 2
  • Total versions: 9
  • Total maintainers: 3
pypi.org: genotype

genotype provides an automated pipipeline for comparinggenotypes from different assays.

  • Versions: 9
  • Dependent Packages: 1
  • Dependent Repositories: 2
  • Downloads: 71 Last month
Rankings
Dependent packages count: 4.7%
Dependent repos count: 11.6%
Average: 16.5%
Stargazers count: 18.5%
Forks count: 19.1%
Downloads: 28.8%
Maintainers (3)
henriks karlnyr clingen
Last synced: 11 months ago

Dependencies

requirements.txt pypi
  • Alchy *
  • Flask ==1.1.1
  • Flask-Alchy *
  • Flask-Bootstrap *
  • Flask-Dance *
  • Flask-Login *
  • Flask-Reverse-Proxy *
  • Flask-SQLAlchemy ==2.1
  • Flask-Security *
  • SQLAlchemy <1.4
  • click *
  • coloredlogs *
  • cython *
  • cyvcf2 *
  • gunicorn *
  • pymysql *
  • pysam *
  • pyyaml *
  • ruamel.yaml *
  • werkzeug <1.0.0
  • wheel *
  • xlrd ==1.2.0
.github/workflows/black.yml actions
  • actions/checkout v2.6.0 composite
  • actions/setup-python v4.3.1 composite
  • psf/black stable composite
.github/workflows/build_and_publish.yml actions
  • actions/checkout v2.6.0 composite
  • actions/setup-python v4.3.1 composite
  • pypa/gh-action-pypi-publish master composite
.github/workflows/build_dockerfile_on_push.yml actions
  • actions/checkout v2.6.0 composite
  • docker/build-push-action v3.2.0 composite
  • docker/login-action v2.1.0 composite
  • docker/setup-buildx-action v2.2.1 composite
.github/workflows/build_dockerfile_on_release.yml actions
  • actions/checkout v2.6.0 composite
  • docker/build-push-action v3.2.0 composite
  • docker/login-action v2.1.0 composite
  • docker/setup-buildx-action v2.2.1 composite
.github/workflows/build_docs.yml actions
  • actions/checkout v2.6.0 composite
  • mhausenblas/mkdocs-deploy-gh-pages master composite
.github/workflows/bumpversion_on_merge_master.yml actions
  • Clinical-Genomics/bump2version-ci v3 composite
.github/workflows/installations.yml actions
  • actions/checkout v2.6.0 composite
  • actions/setup-python v4.3.1 composite
.github/workflows/tests_and_coverage.yml actions
  • actions/checkout v2.6.0 composite
  • actions/setup-python v4.3.1 composite
Dockerfile docker
  • python 3.7-slim build
.github/workflows/deploy_prod.yml actions
.github/workflows/deploy_stage.yml actions
pyproject.toml pypi
poetry.lock pypi
  • alchy 2.2.2
  • atomicwrites 1.4.1
  • attrs 23.2.0
  • babel 2.14.0
  • blinker 1.7.0
  • certifi 2024.2.2
  • cfgv 3.4.0
  • charset-normalizer 3.3.2
  • click 8.1.7
  • colorama 0.4.6
  • coloredlogs 15.0.1
  • cyvcf2 0.30.28
  • distlib 0.3.8
  • dominate 2.9.1
  • filelock 3.13.1
  • flask 1.1.1
  • flask-alchy 0.5.0
  • flask-babelex 0.9.4
  • flask-bootstrap 3.3.7.1
  • flask-dance 3.0.0
  • flask-login 0.5.0
  • flask-mail 0.9.1
  • flask-principal 0.4.0
  • flask-reverse-proxy 0.2.0.2
  • flask-security 3.0.0
  • flask-sqlalchemy 2.1
  • flask-wtf 1.2.1
  • ghp-import 2.1.0
  • gunicorn 21.2.0
  • humanfriendly 10.0
  • identify 2.5.35
  • idna 3.6
  • importlib-metadata 7.0.1
  • itsdangerous 1.1.0
  • jinja2 2.11.2
  • markdown 3.5.2
  • markupsafe 2.0.1
  • mergedeep 1.3.4
  • mkdocs 1.5.3
  • mkdocs-material 8.3.0
  • mkdocs-material-extensions 1.3.1
  • more-itertools 10.2.0
  • nodeenv 1.8.0
  • numpy 1.26.1
  • oauthlib 3.2.2
  • packaging 23.2
  • passlib 1.7.4
  • pathspec 0.12.1
  • platformdirs 4.2.0
  • pluggy 0.13.1
  • pre-commit 3.6.2
  • py 1.11.0
  • pydash 7.0.7
  • pygments 2.17.2
  • pymdown-extensions 10.7
  • pymysql 1.1.0
  • pyreadline3 3.4.1
  • pysam 0.22.0
  • pytest 5.2.0
  • pytest-mock 3.12.0
  • python-dateutil 2.8.2
  • pyyaml 6.0.1
  • pyyaml-env-tag 0.1
  • requests 2.31.0
  • requests-oauthlib 1.3.1
  • ruamel-yaml 0.18.6
  • ruamel-yaml-clib 0.2.8
  • setuptools 69.1.1
  • six 1.16.0
  • speaklater 1.3
  • sqlalchemy 1.3.24
  • typing-extensions 4.9.0
  • urllib3 2.2.1
  • urlobject 2.4.3
  • virtualenv 20.25.1
  • visitor 0.1.3
  • watchdog 4.0.0
  • wcwidth 0.2.13
  • werkzeug 0.16.1
  • wtforms 3.1.2
  • xlrd 1.2.0
  • zipp 3.17.0