MetaboDirect is a Python and R based pipeline for the analysis of Direct Injection FT-ICR Mass Spectrometry data. The MetaboDirect pipeline takes a report file, generated using Formularity (Tolić et al., 2017), and a sample information file as inputs and automatically performs all the analysis described below including: sample filtering, m/z filtering, normalization of intensities, thermodynamic index calculation, annotation of molecular formulas using the KEGG database (Kanehisa & Goto, 2000), statistical analysis and construction of transformation networks using Cytoscape (Shannon et al., 2003).
installation quickstart pipeline use_guide