https://github.com/pgxcentre/genetest

Python package for efficient genetic association analyses
https://github.com/pgxcentre/genetest

bioinformatics genetics genomics gwas phewas regression-models statistics

Last synced: 5 months ago
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Python package for efficient genetic association analyses

• Host: GitHub
• URL: https://github.com/pgxcentre/genetest
• Owner: pgxcentre
• License: other
• Created: 2016-04-14T17:04:22.000Z (about 10 years ago)
• Default Branch: master
• Last Pushed: 2021-10-21T19:46:46.000Z (over 4 years ago)
• Last Synced: 2025-09-08T13:34:33.722Z (10 months ago)
• Topics: bioinformatics, genetics, genomics, gwas, phewas, regression-models, statistics
• Language: Python
• Homepage:
• Size: 6.3 MB
• Stars: 3
• Watchers: 4
• Forks: 2
• Open Issues: 9
• Metadata Files:
  • Readme: README.mkd
  • License: LICENSE.txt

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# genetest - A Python module for statistical genetics

The `genetest` module includes a script that will perform various statistical

analysis on genetics data (*e.g.* hard calls, imputed data, etc.).

## Dependencies

The tool requires a standard [Python](http://python.org/) installation (3.4 or

higher are supported) with the following modules:

1. [numpy](http://www.numpy.org/) version 1.12 or latest

2. [pandas](http://pandas.pydata.org/) version 0.19 or latest

3. [stasmodels](http://statsmodels.sourceforge.net/stable/index.html) version 0.8 or latest

4. [grako](https://github.com/swayf/grako) version 3.10 or latest

5. [geneparse](https://github.com/pgxcentre/geneparse) version 0.1 or latest

The tool has been tested on *Linux* only, but should work on *MacOS* operating

systems as well.

## Documentation

Documentation is available at http://pgxcentre.github.io/genetest/.

## Installation

Using `pip`:

```bash

pip install genetest

```

### Updating

To update the module using `pip`:

```bash

pip install -U genetest

```

## Testing

To test the module, just perform the following command:

```console

$ python -m genetest.tests

...

----------------------------------------------------------------------

Ran 104 tests in 1.684s

OK (skipped=41, expected failures=1)

```