microbetag

Welcome

• About

Modules

• Modules
  • Overview
  • Functional annotations
  • Pathway complementarity
  • Seed scores and complements based on genome-scale draft reconstructions (GEMs)
  • References

Installation

• Install microbetag
  • Where to get what
  • Install MGG Cytoscape
  • Install microbetg_prep tool
  • From source code
  • Install gurobi license

Tutorials

• Input files
  • Abundance table
  • Metadata file
  • Network file
• microbetag on Cytoscape
  • .. using an abundance table
  • .. using an abundance table and a metadata file
  • .. using a co-occurrence network
  • Load networks to Cytoscape and microbetag
• Exploring annotated networks
  • Exploring annotated nodes and edges
  • Investigating nodes’ annotations
  • Investigating edges’ annotations
  • Save your work
• Enrichment analysis
  • Background and MGG implementation
  • How-to

Tutorials - advanced use

• Additional tutorials
  • microbetag preparation steps
  • microbetag using custom genomes
  • Large dataset
  • Run microbetag from Python

FAQ

• Frequently Asked Questions
  • Setting the parameters right
  • I can’t get an annotated network, despite having correct input files and well-tuned parameters
  • Frozen Sending data to server pop-up
  • GTDB and microbetagDB versioning
  • How to read a KEGG map with pathway complementarities ?
  • I am trying to run microbetag locally, but..
  • I have a really large 16S-oriented network. What can I do?
  • Reconstructing GEMs locally
  • Can’t import files on my macOS

Developer Guide

• microbetagDB API
  • Get genome ids for a NCBI Taxonoy Id
  • PhenDB-like traits
    • Get phenotypic traits of a GTDB genome
  • Get pathway complementarities
    • Get pathway complementarities for a pair of genomes
    • Get complements for a pair of species
  • Get seed scores and seed complements
    • Get competition and complementarity score between a pair of NCBI Ids
    • Get competition and complementarity scores between a pair of GEMs
    • Get seed complements between a pair of NCBI Taxonomy Ids, NCBI Genome or PATRIC ids
  • Common errors
• API Reference
  • microbetag
    • Submodules
    • Package Contents
  • parse_module_definitions
    • Module Contents