annotating microbial co-occurrence networks
background, documentation and a use case
beta version
View it on GitHub CytoscapeApp
About
Microbial interactions play a fundamental role in deciphering the underlying mechanisms that govern ecosystem functioning. Co-occurrence networks have been widely used for inferring microbial associations or/and interactions from metagenomic data. However, spurious associations and tool - dependence confine the network inference. The integration of previous evidence or/and knowledge can increase or decrease the confidence level of the retrieved associations. This way, associations can be further investigated and more reliable conclusions can be drawn.
microbetag implements data integration techniques to annotate both the nodes (taxa) and the edges (predicted associations) of such a network to enhance microbial co-occurrence network analysis for amplicon data. Have a look at the modules tab to get an overview of the methods used.
How to use
Cytoscape is a well-established, widely used software for network data integration, analysis, and visualization. microbetag is available as a Cytoscape App; we call the CytoscapeApp MGG. To use it you need to first make sure you have Cytoscape installed on your machine; if not you can do this from the Cytoscape Install page Then, after lunching Cytoscape, you may visit the Cytoscape Appstore and install MGG by pressing the Install button. Alternatively, you may click Apps > App manager.. after lunching Cytoscape, then search for “microbetag” in the pop-up box and click “Install”.
Once MGG is installed, you are ready to use microbetag either on the fly, by providing an OTUs/ASVs (amplicon data) and optionally a network, if you already have one, or locally, if you want to apply the annotations on your own bins/MAGs. In the last case, you will also have to install Docker or Singularity and pull the microbetag image that allows you to do so (see Tutorials for more).
HOW TO USE AND INTERPRET MICROBETAG’s FINDINGS
For a thorough description of the app, please check the Cytoscape App tab.
In addition, microbetag’s annotations are also available through its Application Programming Interface (API). This way, one may have direct access to the microbetagDB and may export annotations for species or pairs of species of interest, without the need of a network.
Contact
For hints on how to use microbetag, ideas for new features and bug reports find us on out matrix space.
Cite us
In prep.
Funding
This project was funded by an EMBO Scientific Exchange Grants and the 3D’omics Horizon project (101000309).
License
microbetag is under GNU General Public License v3.0. For third-party components separate licenses apply. The MGG CytoscapeApp is under Apache License, Version 2.0.