Metabolic and immune markers for precise monitoring of COVID-19 severity and treatment

Andre Figueiredo Rendeiro, Charles Kyriakos Vorkas, Jan Krumsiek, Harjot Singh, Shashi N Kapadia, Luca Vincenzo Cappelli, Maria Teresa Cacciapuoti, Giorgio Inghirami, Olivier Elemento, Mirella Salvatore. Metabolic and immune markers for precise monitoring of COVID-19 severity and treatment. MedRxiv (2021). doi:10.1101/2021.09.05.21263141

⬅️ read the preprint here

Organization

• The data directory contains the assay data (NMR).
• The metadata directory contains metadata relevant to annotate the samples.
• The src directory contains source code used to analyze the data.
• Outputs from the analysis will be present in a results directory, with subfolders pertaining to each part of the analysis as described below.

Reproducibility

Running

To see all available steps type:

$ make help

Makefile for the covid-metabolomics project/package.
Available commands:
help            Display help and quit
requirements    Install Python requirements
convert			[dev] Convert R data to CSV/parquet
analysis		Run project analysis

To reproduce analysis, simply do:

$ make requirements
$ make

If you wish to run a portion of the analysis interactively say with IPython, make sure the repository root is added to your PYTHONPATH to allow importing of the src module. IPython may already do this by default.

Requirements

• Python 3.8+ (running on 3.8.2)
• Python packages as specified in the requirements file - install with make requirements or pip install -r requirements.txt.