CLeaning to Analysis: Reproducibility-based Interface for Traits and Exposures
Project description
CLeaning to Analysis: Reproducibility-based Interface for Traits and Exposures
Free software: 3-clause BSD license
Documentation: https://www.hall-lab.org/clarite-python/.
Installation
In order to use the ewas_r function, it is recommended to install CLARITE using Conda:
Create and activate a conda environment with python 3.6 or 3.7:
$ conda create -n clarite python=3.7 $ conda activate clarite
Install rpy2 (optional). CLARITE has a version of the EWAS function that calls R code using the survey library:
$ conda install -c conda-forge rpy2
Install CLARITE:
$ pip install clarite
Install required R packages (such as survey) (optional):
$ clarite-cli utils install-r-packages
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
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