Basic Install

At the command line:

$ pip install clarite

Running R code from CLARITE

In order to use the ewas_r function, it is recommended to install CLARITE 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
  3. Install CLARITE:

    $ pip install clarite
  4. Install required R packages (such as survey) (optional):

    $ clarite-cli utils install-r-packages