metabolomics-tools

A compilation of code helpful in filtering, assessing data quality, and conducting first pass metabolomics analysis.

Divided into:

• First pass filtering: takes data directly from MZmine, filters based on retention time, cleans up file names, removes unwanted samples, filtering based on presence in the QCs (both by number and by CV), removing features present in the process blanks.
• First pass data analysis: takes data directly from first pass filtering and surveys and handles missing data, imputes missing values, assesses data quality, clusters features coming from the same metabolite using notame, transforms data, runs and visualizes PCAs, and conducts basic univarite analysis.

You also might be interested in the following tutorials:

• Exploring the notame package, preprocessing: by Daniel Quiroz Moreno
• Exploring the notame package, statistical analyses: by Daniel Quiroz Moreno

Or some tools we've created:

• MS2extract: an R package developed by Daniel Quiroz Moreno to extract MS/MS spectra for the creation of in-house libraries.