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        "description": "[![Build Status](https://travis-ci.org/biocore/DEICODE.svg?branch=master)](https://travis-ci.org/biocore/DEICODE)\n[![Coverage Status](https://coveralls.io/repos/github/biocore/DEICODE/badge.svg?branch=master)](https://coveralls.io/github/biocore/DEICODE?branch=master)\n\nDEICODE is a tool box for running Robust Aitchison PCA on sparse compositional omics datasets, linking specific features to beta-diversity ordination. \n\n## Installation\n\nTo install the most up to date version of deicode, run the following command\n\n    # pip (only supported for QIIME2 >= 2018.8)\n    pip install deicode\n\n    # conda (only supported for QIIME2 >= 2019.1)\n    conda install -c conda-forge deicode \n\n**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.\n\n## Using DEICODE as a standalone tool\n\n```\n$ deicode --help\nUsage: deicode [OPTIONS]\n\n  Runs RPCA with an rclr preprocessing step.\n\nOptions:\n  --in-biom TEXT               Input table in biom format.  [required]\n  --output-dir TEXT            Location of output files.  [required]\n  --n_components INTEGER       The underlying low-rank structure (suggested: 1\n                               < rank < 10) [minimum 2]  [default: 3]\n  --min-sample-count INTEGER   Minimum sum cutoff of sample across all\n                               features  [default: 500]\n  --min-feature-count INTEGER  Minimum sum cutoff of features across all\n                               samples  [default: 10]\n  --max_iterations INTEGER         The number of iterations to optimize the\n                               solution (suggested to be below 100; beware of\n                               overfitting) [minimum 1]  [default: 5]\n  --help                       Show this message and exit.\n```\n\n## Using DEICODE inside [QIIME 2](https://qiime2.org/)\n\n* The QIIME2 forum tutorial can be found [here](https://forum.qiime2.org/t/robust-aitchison-pca-beta-diversity-with-deicode/8333).\n* The official plugin docs and tutorial can be found [here](https://library.qiime2.org/plugins/deicode).\n* The in-repo tutorial can be found [here](https://github.com/biocore/DEICODE/blob/master/ipynb/tutorials/moving-pictures.md).\n\n## Other Resources\n\n* [Aitchison Distance Introduction](https://github.com/biocore/DEICODE/blob/master/ipynb/introduction.ipynb)\n\n- 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).\n- Transforms and PCoA : [Scikit-bio](http://scikit-bio.org)\n- Data For Examples : [Qiita](https://qiita.ucsd.edu/)\n\n#### Simulation and Benchmarking\n\n* [simulations and case studies](https://github.com/cameronmartino/deicode-benchmarking)\n\n\n",
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