gemelli
Gemelli is a toolbox for running tensor factorization on sparse compositional omics datasets. Gemelli performs unsupervised dimensionality reduction of spatiotemporal microbiome data. The output of gemelli helps to resolve spatiotemporal subject variation and the biological features that separate them.
install guide:
Installation
To install the most up to date version of deicode, run the following command
# pip (only supported for QIIME2 >= 2018.8)
pip install gemelli
Note: that gemelli is not compatible with python 2, and is compatible with Python 3.4 or later.
Documentation
Tutorials
There are several ways to run CTF through gemelli. Here we provide a tutorial of a time series IBD data set in each of the different formats:
Tutorials with QIIME2
Standalone tutorial outside of QIIME2
The publication associated with this plugin can be found at https://www.nature.com/articles/s41587-020-0660-7