clarite

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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

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

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

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