Canonically pronouced nice

gneiss is a compositional statistics and visualization toolbox. See here for API documentation.

Note that gneiss is not compatible with python 2, and is compatible with Python 3.4 or later. gneiss is currently in alpha. We are actively developing it, and backward-incompatible interface changes may arise.

To install this package, it is recommended to use conda. An environment can installed as follows

conda create -n gneiss_env gneiss python=3.5 -c biocore -c qiime2

IPython notebooks demonstrating some of the modules in gneiss can be found as follows

• What are balances
• Linear regression on balances in the 88 soils
• Linear mixed effects models on balances in a CF study

If you use this software package in your own publications, please cite it at

Morton JT, Sanders J, Quinn RA, McDonald D, Gonzalez A, Vázquez-Baeza Y, 
Navas-Molina JA, Song SJ, Metcalf JL, Hyde ER, Lladser M, Dorrestein PC, 
Knight R. 2017. Balance trees reveal microbial niche differentiation. 
mSystems 2:e00162-16. https://doi.org/10.1128/mSystems.00162-16.