Welcome to MEANtools documentation!

MEANtools (Metabolite Anticipation tools) is a Python based omics data integration workflow that predicts biosynthetic pathways by integrating genomics, transcriptomics and metabolomics data with the reaction (RetroRules) and structural (LOTUS) databases. It offers a simple and intuitive API.

• Usage section will provide more information on different input and output parameters.

• Installation will help you with the installation of MEANtools.

• Results will guide you through results step-by-step.

• Tutorial is a step by step turoial of MEANtools with a small demo data.

Note

This project is under active development so the documentation will be updated regulalrly.

Contents

• Installation
• Usage
  • MEANtools workflow
  • Databases availability
  • Database Preparation
  • Input Description
  • Omics data preparation
  • Prediction
• Results
  • Format Database
  • Correlation
  • Structure database mapping
  • Map mass trantions
  • Visualization
• Tutorial
  • Step 1 Query the LOTUS database
  • Step 2 Correlation analysis
  • Step 3 Merge Functional Clusters
  • Step 4 Map mass transitions
  • Step 5 Predict reaction steps
  • Step 6 Generate reaction graphics
  • Generate reaction graphics with reaction likelihood scores