Quick start

To quickly run the MetaboDirect pipeline use the following command.

metabodirect DATA_FILE METADATA_FILE -g GROUPING_VARIABLE

Check metabodirect in the User’s Guide to learn more about the required input data and the analysis options that are offered.

Information about the arguments can be obtained using the -h/–help function.

metabodirect -h

Example using test data

Example data can be downloaded from the MetaboDirect repository example directory, or from the command line with:

# Report file
wget https://raw.githubusercontent.com/Coayala/MetaboDirect/main/example/Report.csv --no-check-certificate

# Metadata file
wget https://raw.githubusercontent.com/Coayala/MetaboDirect/main/example/metadata.csv --no-check-certificate

Try analizing example data using:

metabodirect Report.csv metadata.csv -o test -m 200 400 -g Habitat Depth -t -k