clarite 1.0.1

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

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, R must be installed along with the survey library. This can be done manually or using Conda:

Manually

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.

Using Conda

1. Create and activate a conda environment with python 3.6 or 3.7:

   $ conda create -n clarite python=3.7
   $ conda activate clarite

2. 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
   $ conda install -c bioconda r-survey

3. Install CLARITE:

   $ pip install clarite

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