EWAS-NHS

Paper: A Systematic Comprehensive Longitudinal Evaluation of Dietary Factors Associated with Coronary Heart Disease

Authors: Soodabeh Milanlouei, Giuia Menichetti, Yanping Li, Joseph Loscalzo, Walter C. Willett, Albert-Laszlo Barabasi

Status: Under Review

System Requirements

Hardware Requirements

All the codes provided require a standard computer with enough RAM to support the operations. For minimal performance, this will be a computer with about 16 GB of RAM and 4 cores. For optimal performance, we recommend a computer with the following specifications:

RAM: 100+ GB

CPU: 32+ cores

Software Requirements

Provided codes have been tested on the following systems:

Mac OSX (10.14.6)

Windows: 7+

Linux: Ubuntu 16.04

Software versions used:

• Python: 2.7.16
• R: 3.4.0
• MATLAB: 9.6

Installation Guide

In Python:

pip install pandas
pip install scipy.stats 

Version Numbers for Python Packages

• pandas: 0.23.4
• scipy.stats: 0.18.1

In R:

install.packages(c('car', 'bestNormalize', 'data.table', 'datasets', 'devtools', 'doParallel', 'foreach', 'haven', 'MASS', 'parallel', 'survival', 'zoo', 'adegenet', 'glmnet', 'corrplot))

Version Numbers for R Packages

• car: 3.0.3
• bestNormalize: 1.3.0
• data.table: 1.11.8
• datasets: 3.5.0
• devtools: 2.0.1
• doParallel: 1.0.14
• foreach: 1.4.4
• haven: 2.0.0
• MASS: 7.3.51.1
• parallel: 3.5.0
• survival: 2.43.3
• zoo: 1.8.4
• adegenet: 2.1.1
• glmnet: 2.0.16
• corrplot: 0.84

Typical install time on a normal desktop computer for all Python and R packages is less than 10 minutes.