clarite 2.3.6

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

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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

More realistically, perform some QC first:

Genotype data is supported via Pandas-Genomics

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, feel free to open an Issue.

Citing CLARITE

1. Lucas AM, et al (2019) CLARITE facilitates the quality control and analysis process for EWAS of metabolic-related traits. 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. Pacific Symposium on Biocomputing: 25, 659