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charger

Characterization of Germline variants

https://github.com/ding-lab/charger

Science Score: 23.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    6 of 11 committers (54.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.1%) to scientific vocabulary

Keywords

acmg annotations bioinformatics characterization clinical clinvar diseases exac germline-variants gnomad pathogenic-variants pathogenicity variants vep
Last synced: 6 months ago · JSON representation

Repository

Characterization of Germline variants

Basic Info
Statistics
  • Stars: 98
  • Watchers: 18
  • Forks: 37
  • Open Issues: 10
  • Releases: 0
Topics
acmg annotations bioinformatics characterization clinical clinvar diseases exac germline-variants gnomad pathogenic-variants pathogenicity variants vep
Created over 10 years ago · Last pushed almost 4 years ago
Metadata Files
Readme Changelog License

README.md

CharGer

⚠️ NOTICE: To use the most recent stable CharGer (version v0.5.4; Python 2.7 only), please refer to the installation instructions and source code at commit 7d7d291 or tag v0.5.4. Python 3 compatible CharGer is still under development.

CharGer (Characterization of Germline variants) is a software tool for interpreting and predicting clinical pathogenicity of germline variants. CharGer gathers evidence from databases and annotations, provided by local tools and files or via ReST APIs, and classifies variants according to ACMG guidelines for assessing variant pathogenicity. User-designed pathogenicity criteria can be incorporated into CharGer’s flexible framework, thereby allowing users to create a customized classification protocol.

If you use CharGer, please cite our publication so we can continue to support CharGer development:

Scott, A.D., Huang, K.-L., Weerasinghe, A., Mashl, R.J., Gao, Q., Martins Rodrigues, F., Wyczalkowski, M.A., and Ding, L. (2018). CharGer: clinical Characterization of Germline variants. Bioinformatics 35, 865–867. DOI: https://doi.org/10.1093/bioinformatics/bty649

Installation

⚠️ Version 0.6.0+ is still UNDER DEVELOPMENT and INCOMPLETE.

CharGer requires Python 3.6+. Use pip to install CharGer:

pip install charger

Alternatively, use conda with bioconda channels configured:

conda install charger

Usage

charger -h

Visit CharGer's documentations for its detailed usage.

License

CharGer is made by Ding Lab under GNU GPL v3.0 only license.

Owner

  • Name: Li Ding's Lab
  • Login: ding-lab
  • Kind: organization
  • Email: lding@wustl.edu
  • Location: St. Louis, MO, USA

Li Ding's Lab at the Washington University School of Medicine

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 405
  • Total Committers: 11
  • Avg Commits per committer: 36.818
  • Development Distribution Score (DDS): 0.548
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Liang-Bo Wang l****g@w****u 183
Adam David Scott a****m@a****m 100
Fernanda Martins Rodrigues f****a@w****u 39
Kuan h****n@g****m 39
R. Jay Mashl r****l@w****u 21
Adam_D_Scott a****t@w****u 13
Amila_Weerasinghe a****a@w****u 3
Amila Weerasinghe a****w@g****m 2
Adam D Scott a****t@g****u 2
mmoisse m****e 2
Adam David Scott a****t@g****m 1
Committer Domains (Top 20 + Academic)
wustl.edu: 5 genome.wustl.edu: 1 adamscottphd.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 37
  • Total pull requests: 21
  • Average time to close issues: 3 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 27
  • Total pull request authors: 3
  • Average comments per issue: 1.76
  • Average comments per pull request: 0.29
  • Merged pull requests: 13
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • yubau1112 (4)
  • rescuz (4)
  • nah2025 (3)
  • mingoo426 (2)
  • NTNguyen13 (2)
  • lihm1 (1)
  • rhshah (1)
  • xuanzhu1213 (1)
  • luwening (1)
  • laura-budurlean (1)
  • ccwang002 (1)
  • mmoisse (1)
  • ekofman (1)
  • JYE-Lee (1)
  • altundal19 (1)
Pull Request Authors
  • fernanda-rodrigues (13)
  • mmoisse (7)
  • icebert (1)
Top Labels
Issue Labels
BioMine-related-issue (2) help wanted (2) question (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 49 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 4
  • Total maintainers: 2
pypi.org: charger

Characterization of Germline variants

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 49 Last month
Rankings
Forks count: 6.3%
Stargazers count: 7.4%
Dependent packages count: 10.0%
Average: 15.7%
Dependent repos count: 21.7%
Downloads: 32.8%
Maintainers (2)
adamds lbwang2
Last synced: 6 months ago

Dependencies

poetry.lock pypi
  • alabaster 0.7.12 develop
  • atomicwrites 1.4.0 develop
  • babel 2.9.1 develop
  • backports.entry-points-selectable 1.1.0 develop
  • black 21.9b0 develop
  • certifi 2021.5.30 develop
  • cfgv 3.3.1 develop
  • charset-normalizer 2.0.6 develop
  • distlib 0.3.3 develop
  • docutils 0.17.1 develop
  • filelock 3.0.12 develop
  • flake8 3.9.2 develop
  • ghp-import 2.0.1 develop
  • identify 2.2.15 develop
  • idna 3.2 develop
  • imagesize 1.2.0 develop
  • iniconfig 1.1.1 develop
  • isort 5.9.3 develop
  • jinja2 3.0.1 develop
  • markupsafe 2.0.1 develop
  • mccabe 0.6.1 develop
  • mypy 0.910 develop
  • mypy-extensions 0.4.3 develop
  • nodeenv 1.6.0 develop
  • packaging 21.0 develop
  • pathspec 0.9.0 develop
  • platformdirs 2.3.0 develop
  • pluggy 1.0.0 develop
  • pre-commit 2.15.0 develop
  • py 1.10.0 develop
  • pycodestyle 2.7.0 develop
  • pyflakes 2.3.1 develop
  • pygments 2.10.0 develop
  • pyparsing 2.4.7 develop
  • pytest 6.2.5 develop
  • python-dateutil 2.8.2 develop
  • pytz 2021.1 develop
  • pyyaml 5.4.1 develop
  • regex 2021.8.28 develop
  • requests 2.26.0 develop
  • six 1.16.0 develop
  • snowballstemmer 2.1.0 develop
  • sphinx 4.2.0 develop
  • sphinx-argparse 0.3.1 develop
  • sphinx-issues 1.2.0 develop
  • sphinxcontrib-applehelp 1.0.2 develop
  • sphinxcontrib-devhelp 1.0.2 develop
  • sphinxcontrib-htmlhelp 2.0.0 develop
  • sphinxcontrib-jsmath 1.0.1 develop
  • sphinxcontrib-qthelp 1.0.3 develop
  • sphinxcontrib-serializinghtml 1.1.5 develop
  • toml 0.10.2 develop
  • tomli 1.2.1 develop
  • typed-ast 1.4.3 develop
  • urllib3 1.26.7 develop
  • virtualenv 20.8.0 develop
  • attrs 21.2.0
  • click 8.0.1
  • colorama 0.4.4
  • coloredlogs 15.0.1
  • cyvcf2 0.30.11
  • humanfriendly 10.0
  • importlib-metadata 1.7.0
  • loguru 0.5.3
  • numpy 1.21.1
  • pyreadline 2.1
  • pyreadline3 3.3
  • pysam 0.16.0.1
  • typing-extensions 3.10.0.2
  • win32-setctime 1.0.3
  • zipp 3.5.0
pyproject.toml pypi
  • black ^21.9b0 develop
  • flake8 ~3.9 develop
  • ghp-import ^2.0.1 develop
  • importlib_metadata ^1.5.0 develop
  • isort ^5.9.3 develop
  • mypy ^0.910 develop
  • pre-commit ^2.0.0 develop
  • pytest ^6.2.5 develop
  • sphinx ~4.2 develop
  • sphinx-argparse ^0.3.1 develop
  • sphinx-issues ^1.2.0 develop
  • attrs ^21.0
  • cyvcf2 ^0.30.0
  • loguru ~0.5
  • pysam ^0.16.0.1
  • python >=3.7,<4.0
  • typing-extensions ~3.10