Metadata-Version: 1.2
Name: rhapsody
Version: 0.1.0
Summary: Microbe-metabolite interactions through neural networks
Home-page: UNKNOWN
Author: gneiss development team
Author-email: jamietmorton@gmail.com
Maintainer: gneiss development team
Maintainer-email: jamietmorton@gmail.com
License: BSD-3-Clause
Description: # rhapsody
        Neural networks for estimating microbe-metabolite co-occurence probabilities.
        
        # Installation
        ```
        conda create -n mae python=3.5 tensorflow numpy scipy pandas scikit-bio tqdm pip
        conda install -n mae biom-format -c conda-forge
        source activate mae
        pip install h5py git+https://github.com/mortonjt/rhapsody.git
        ```
        
        If you are getting errors, it is likely because you have garbage channels under your .condarc.  Make sure to delete your .condarc -- you shouldn't need it.
        
        # Getting started
        
        To get started you can run a quick example as follows.  This will generate
        microbe-metabolite conditional probabilities that are accurate up to rank.
        
        ```
        rhapsody autoencoder \
        	--otu-file data/otu.biom \
        	--metabolite-file data/ms.biom \
        	--summary-dir summary \
        	--results-file cv-results.csv \
        	--ranks-file ranks.csv
        ```
        
        While this is running, you can open up another session and run `tensorboard --logdir .` for diagnosis.
        
        See the following url for a more complete tutorial with real datasets.
        
        https://github.com/knightlab-analyses/multiomic-cooccurences
        
        More information can found under `rhapsody --help`
        
        # Qiime2 plugin
        
        If you want to make this qiime2 compatible, install this in your
        qiime2 conda environment and run the following
        
        ```
        qiime dev refresh-cache
        ```
        
        This should allow your q2 environment to recognize rhapsody.  To test run
        the qiime2 plugin, run the following commands
        
        ```
        qiime tools import \
        	--input-path data/otu.biom \
        	--output-path otu.qza \
        	--type FeatureTable[Frequency]
        
        qiime tools import \
        	--input-path data/ms.biom \
        	--output-path ms.qza \
        	--type FeatureTable[Frequency]
        
        qiime rhapsody autoencoder \
        	--i-microbes otu.qza \
        	--i-metabolites ms.qza \
        	--o-conditional-ranks ranks.qza
        ```
        
        More information can found under `qiime rhapsody --help`
        
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-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
