CLARITE-GUI

A GUI Version of CLARITE

Full documentation on ReadTheDocs.io

Running

Executables are available under releases.

To run using python:

1. Download or clone this repository and enter the folder

2. Ensure pipenv is installed

   pip install pipenv

3. Create/update the pipenv

   pipenv update

4. Run:

   pipenv run python main.py

Known Issues

• Using the 'r_survey' regression method in 'ewas'
  • This will currently raise an error "signal only works in main thread". This should be resolved when this pull request is merged into rpy2
• Build not available for MacOS
  • Due to Big Sur difficulties, which may be resolved in a future version of PyInstaller
• Statsmodels/PyInstaller incompatibility
  • Will be fixed in the next release of PyInstaller due to a new hook for statsmodels

Build Notes

Windows

pipenv run pyinstaller -F --name=CLARITE --icon=clarite_logo.ico main.py ./dist/CLARITE.exe

Mac - Currently broken on Big Sur

pipenv run pyinstaller -F --name=CLARITE --icon=clarite_logo.ico --hidden-import cmath --windowed main.py open ./dist/CLARITE.app

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