Welcome to MetaboDirect’s documentation!

Introduction

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
  • Required modules
• Quick start
  • Example using test data
• MetaboDirect pipeline
  • (Optional Step) Test normalization methods
  • 1. Data pre-processing
  • 1. Data diagnostics
  • 3. Data exploration
  • 4. Diversity analysis
  • 5. Statistical analysis
  • 6. Transformation networks
• User’s Guide
  • metabodirect
  • test_normalization
  • create_networks