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 python=3
gneiss then can be installed as follows
source activate gneiss_env
conda install pyqt=4.11.4
pip install gneiss
gneiss can also be installed through conda
conda install -c biocore gneiss
To run through the tutorials, you'll need a few more packages, namely seaborn, biom-format and h5py.
These packages can be installed with conda as follows
conda install seaborn h5py
pip install biom-format
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
- Linear mixed effects models on balances in a PTSD 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.