semvec/pypi-packages huggingface dataset:
clarite 2.4.1
CLeaning to Analysis: Reproducibility-based Interface for Traits and Exposures
License: BSD-3-Clause
Requires Python: <3.13,>=3.10

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   :alt: CLARITE Logo

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CLeaning to Analysis: Reproducibility-based Interface for Traits and Exposures
==============================================================================

* Free software: 3-clause BSD license
* Documentation: https://www.hall-lab.org/clarite-python/.

Examples
--------

**Run an EWAS in a few lines of code**

.. image:: docs/source/_static/code/quick_ewas.png

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**More realistically, perform some QC first:**

.. image:: docs/source/_static/code/filters.png

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**Genotype data is supported via Pandas-Genomics**

.. image:: docs/source/_static/code/gwas.png

Installation
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In order to use the *r_survey* regression_kind in the *ewas* function, R must be installed along with the *survey* library.

1. Install R and ensure it is accessible from the command line.  You may need to add its location to the PATH environmental variable.
2. Use *install.packages* in R to install the *survey* library.

Questions
---------
If you have any questions not answered by the `documentation <https://clarite-python.readthedocs.io/en/latest/>`_,
feel free to open an `Issue <https://github.com/HallLab/clarite-python/issues>`_.

Citing CLARITE
--------------

1.
Lucas AM, et al (2019)
`CLARITE facilitates the quality control and analysis process for EWAS of metabolic-related traits. <https://www.frontiersin.org/article/10.3389/fgene.2019.01240>`_
*Frontiers in Genetics*: 10, 1240

2.
Passero K, et al (2020)
`Phenome-wide association studies on cardiovascular health and fatty acids considering phenotype quality control practices for epidemiological data. <https://www.worldscientific.com/doi/abs/10.1142/9789811215636_0058>`_
*Pacific Symposium on Biocomputing*: 25, 659