Metadata-Version: 2.1
Name: deicode
Version: 0.1.6
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
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
Requires-Dist: numpy (>=1.12.1)
Requires-Dist: click
Requires-Dist: pandas (>=0.10.0)
Requires-Dist: scipy (>=0.19.1)
Requires-Dist: nose (>=1.3.7)
Requires-Dist: scikit-learn (>=0.18.1)
Requires-Dist: scikit-bio (>0.5.3)
Requires-Dist: biom-format
Requires-Dist: h5py

[![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 QIIME2 >= 2018.8)
    pip install deicode

    # conda (only supported for QIIME2 >= 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

* The QIIME2 forum tutorial can be found [here](https://forum.qiime2.org/t/robust-aitchison-pca-beta-diversity-with-deicode/8333).
* The official plugin docs and tutorial can be found [here](https://library.qiime2.org/plugins/deicode).
* The in-repo tutorial can be found [here](https://github.com/biocore/DEICODE/blob/master/ipynb/tutorials/moving-pictures.md).

## Other Resources

* [Aitchison Distance Introduction](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 and case studies](https://github.com/cameronmartino/deicode-benchmarking)

