Metadata-Version: 1.2
Name: deicode
Version: 0.1.4
Summary: Robust Aitchison compositional biplots from sparse count data
Home-page: UNKNOWN
Author: deicode development team
Author-email: cameronmartino@gmail.com
Maintainer: deicode development team
Maintainer-email: cameronmartino@gmail.com
License: BSD-3-Clause
Description: [![Build Status](https://travis-ci.org/biocore/DEICODE.svg?branch=master)](https://travis-ci.org/biocore/DEICODE)
        [![Coverage Status](https://coveralls.io/repos/github/biocore/DEICODE/badge.svg?branch=master)](https://coveralls.io/github/biocore/DEICODE?branch=master)
        
        DEICODE is a tool box for running Robust Aitchison PCA on sparse compositional omics datasets, linking specific features to beta-diversity ordination. 
        
        ## Installation
        
        To install the most up to date version of deicode, run the following command
        
            # pip (only supported for Qiime >= 2018.8)
            pip install deicode
        
            # conda (only supported for Qiime >= 2019.1)
            conda install -c conda-forge deicode 
        
        **Note**: that deicode is not compatible with python 2, and is compatible with Python 3.4 or later. deicode is currently in alpha. We are actively developing it, and backward-incompatible interface changes may arise.
        
        ## Qiime2 tutorial
        
        **Note**: the official plugin docs and tutorial can be found [here](https://library.qiime2.org/plugins/q2-deicode).
        
        * [Sleep Apnea Biplots](https://github.com/biocore/DEICODE/blob/master/ipynb/sleep_apnea/SleepApnea-qiime2-tutorial.md)
        
        ## Other Resources
        
        * [What is Robust Aitchison RPCA](https://github.com/biocore/DEICODE/blob/master/ipynb/introduction.ipynb)
        
        - The code for OptSpace was translated to python from a [MATLAB package](http://swoh.web.engr.illinois.edu/software/optspace/code.html) maintained by Sewoong Oh (UIUC).
        - Transforms and PCoA : [Scikit-bio](http://scikit-bio.org)
        - Data For Examples : [Qiita](https://qiita.ucsd.edu/)
        
        #### Simulation and Benchmarking
        
        * [simulations](https://github.com/biocore/DEICODE/tree/master/benchmarking/simulations)
        * [case studies](https://github.com/biocore/DEICODE/tree/master/benchmarking/case_studies)
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: BSD License
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
