QIIME 2 plugin for applying the microbiome age model trained in the meta-analysis or AGP data to the new microbiome studies.
Read more about the method in our paper:
- Huang S, Haiminen N, Carrieri A-P, Hu R, Jiang L, Parida L, Russell B, Allaband C, Zarrinpar A, Vázquez-Baeza Y, Belda-Ferre P, Zhou H, Kim H-C, Swafford AD, Knight R, Xu ZZ. 2020. Human skin, oral, and gut microbiomes predict chronological age. mSystems 5:e00630-19. https://doi.org/10.1128/mSystems.00630-19.
You can install this plugin with conda or by cloning this repo and installing manually.
You need to have QIIME 2 version 2019.1 or later (though earlier versions of this plugin work with earlier versions of QIIME 2).
Also, regardless of which way you install, you need to be in a QIIME 2 environment for this to work.
Install QIIME 2 and activate the QIIME 2 virtual environment (source activate qiime2-2020.8) before installing this plugin.
To install from conda, run:
conda install -c xx q2_microbiome_age
To install from this repo, clone the repo to your computer, cd into the main directory, and run:
python setup.py install
You can check that the installation worked by typing qiime on the command line.
The microbiome_age plugin should show up in the list of available plugins.
The only method in this plugin is microbiome_age, which predict the microbiome age for input samples based on the regression model trained in the larger data.
You'll need to prepare your ASV table and metadata file for use with this plugin. Your ASV table should be imported as a QIIME 2 artifact, with ASVs in rows and samples in columns.