microbetag

Welcome

• About
• Modules
• Usage modes

Installation

• Install microbetag
  • Where to get what
  • Install MGG Cytoscape
  • Install stand-alone microbetag
  • Install microbetag_prep tool
  • Further dependencies

Tutorials: core topics

• microbetag on Cytoscape
  • MGG and microbetag versioning map
• Input files and mandatory parameters
  • Abundance table
  • Metadata file
  • Network file
  • Basic parameters
• Exploring annotated networks
  • Exploring annotated nodes and edges
  • Visual style
  • Investigating nodes’ annotations
  • Investigating edges’ annotations
  • Save your work
• Enrichment analysis
  • Background and MGG implementation
  • How-to
• Loading networks
  • Load an edge list to be used with microbetag
  • Load edge list coming from the microbetag preparation step
  • Load already microbetag-annotated networks!

Tutorials: on-the-fly

• .. using an abundance table
• .. using an abundance table and a metadata file
• .. using a co-occurrence network
• microbetag preparation steps
  • The preparation step
  • I/O folder
  • An example case
• Large dataset
  • 16S rRNA data of hundreds of sub-gingival plaque samples from a Qiita project

Tutorials: stand-alone

• 🎯 microbetag locally
  • ✅ Check availability
  • Use microbetag’s features as a library
  • 🤖 Use microbetag API programmatically
• .. using custom genomes
  • Input and config.yml files
  • Output
• Configuration file
• Building GENREs on microbetag
  • using modelseedpy and your bins
  • using modelseedpy and your already RAST annotated genomes
  • using carveme
• on a container
  • .. using Docker
  • .. using Singularity/Apptainer

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?
  • Can’t import files on my macOS

Developer Guide

• microbetagDB API
  • Get genome IDs for a NCBI Taxonomy ID
  • 🧬 Genome-based predicted phenotypic traits
  • 🧩 Get pathway complementarities
  • Get seed scores and complements
    • Get competition and complementarity seed scores
    • Get seed complements
  • Common errors
• API Reference
  • microbetag
    • Submodules
    • Attributes
    • Package Contents
  • parse_module_definitions
    • Attributes
    • Functions
    • Module Contents