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pygenclean

Automated genetic data clean up procedure in Python.

https://github.com/lemieuxl/pygenclean

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
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.7%) to scientific vocabulary

Keywords

bioinformatics genetics genomics
Last synced: 6 months ago · JSON representation

Repository

Automated genetic data clean up procedure in Python.

Basic Info
  • Host: GitHub
  • Owner: lemieuxl
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 15.7 MB
Statistics
  • Stars: 3
  • Watchers: 3
  • Forks: 2
  • Open Issues: 2
  • Releases: 7
Topics
bioinformatics genetics genomics
Created about 11 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.mkd 

[![PyPI version](https://badge.fury.io/py/pyGenClean.svg)](http://badge.fury.io/py/pyGenClean)


# pyGenClean - Automated Data Clean Up #

`pyGenClean` is an informatics tool to facilitate and standardize the genetic
data clean up pipeline with genotyping array data. In conjunction with a source
batch-queuing system, the tool minimizes data manipulation errors, it
accelerates the completion of the data clean up process and it provides
informative graphics and metrics to guide decision making for statistical
analysis.

If you use `pyGenClean` in you project, please cite the published paper
describing the tool:

> Lemieux Perreault LP, Provost S, Legault MA, Barhdadi A, Dubé MP (2013)
> pyGenClean: efficient tool for genetic data clean up before association testing.
> *Bioinformatics*, **29**(13): 1704-1705
> [DOI:[10.1093/bioinformatics/btt261](http://dx.doi.org/10.1093/bioinformatics/btt261)]



## Documentation##

Documentation is available from
[http://lemieuxl.github.io/pyGenClean/](http://lemieuxl.github.io/pyGenClean/).



## Dependencies ##

Here are the dependencies that must be installed before _pyGenClean_:

*   [Python](http://python.org/) (version 2.7)
*   [numpy](http://www.numpy.org/) (version 1.6.2 or latest)
*   [matplotlib](http://matplotlib.org/) (version 1.2.0 or latest)
*   [scipy](http://www.scipy.org/) (version 0.11.0 or latest)
*   [scikit-learn](http://scikit-learn.org/stable/) (version 0.12.1 or latest)
*   [Jinja2](http://jinja.pocoo.org/docs/dev/) (version 2.8 or latest)
*   [PLINK](http://pngu.mgh.harvard.edu/~purcell/plink/) (1.07)



## Installation ##

For Linux users, we recommend installing `pyGenClean` in a Python
[virtualenv](http://pypi.python.org/pypi/virtualenv) (virtual environment).

`pyGenClean` should work on Windows and MacOS, even though it hasn't been fully
tested for full compatibility. It has been tried on Windows XP (32 bits) and
Windows 7 (64 bits, but with a 32 bits Python 2.7 installation) without known
problems.

For a step by step installation on both Linux and Windows operation systems, see
`pyGenClean` documentation, located [here](http://lemieuxl.github.io/pyGenClean/#installation).

Owner

  • Name: Louis-Philippe Lemieux Perreault
  • Login: lemieuxl
  • Kind: user
  • Location: Canada
  • Company: Beaulieu-Saucier Pharmacogenomics Centre - Montreal Heart Institute

GitHub Events

Total
  • Push event: 21
Last Year
  • Push event: 21

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 378
  • Total Committers: 2
  • Avg Commits per committer: 189.0
  • Development Distribution Score (DDS): 0.011
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Louis-Philippe Lemieux Perreault l****t@s****g 374
Louis-Philippe Lemieux Perreault L****t@s****g 4
Committer Domains (Top 20 + Academic)
statgen.org: 2

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 27
  • Total pull requests: 0
  • Average time to close issues: about 2 months
  • Average time to close pull requests: N/A
  • Total issue authors: 4
  • Total pull request authors: 0
  • Average comments per issue: 1.04
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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
  • lemieuxl (20)
  • jgrundstad (4)
  • provosts (2)
  • willmclaren (1)
Pull Request Authors
Top Labels
Issue Labels
bug (13) enhancement (11)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 15 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 6
  • Total maintainers: 1
pypi.org: pygenclean

Automated data clean up pipeline for genetic data

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 15 Last month
Rankings
Dependent packages count: 10.0%
Dependent repos count: 21.7%
Forks count: 22.6%
Average: 24.0%
Stargazers count: 25.0%
Downloads: 40.7%
Maintainers (1)
lemieuxl
Last synced: 6 months ago

Dependencies

setup.py pypi
  • Jinja2 *
  • matplotlib *
  • scipy *