Skip to main content

Deep Learning package using the phylogenetic tree information for microbiome data analysis.

Project description

Build Coverage Version

Deep Learning package using the phylogenetic tree information for microbiome abandunce data analysis.

Installation

Prerequisites

  • python >= 3.5

  • Tensorflow

  • Keras

Install DeepBiome

At the command line:

# for python 3.x

$ pip3 install git+https://github.com/Young-won/deepbiome.git

Features

  • deepbiome.deepbiome_train(log, network_info, path_info, number_of_fold=None, max_queue_size=10, workers=1, use_multiprocessing=False)

    Function for training the deep neural network with phylogenetic tree weight regularizer.

    It uses microbiome abundance data as input and uses the phylogenetic taxonomy to guide the decision of the optimal number of layers and neurons in the deep learning architecture.

  • deepbiome.deepbiome_test(log, network_info, path_info, number_of_fold=None, max_queue_size=10, workers=1, use_multiprocessing=False)

    Function for testing the pretrained deep neural network with phylogenetic tree weight regularizer.

    If you use the index file, this function provide the evaluation using test index (index set not included in the index file) for each fold. If not, this function provide the evaluation using the whole samples.

  • deepbiome.deepbiome.deepbiome_prediction(log, network_info, path_info, num_classes, number_of_fold=None, max_queue_size=10, workers=1, use_multiprocessing=False)

    Function for prediction by the pretrained deep neural network with phylogenetic tree weight regularizer.

Credits

This package was builded on the Keras and the Tensorflow packages.

This package was created with Cookiecutter and the NSLS-II/scientific-python-cookiecutter project template.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

deepbiome-1.0.0.tar.gz (61.1 kB view hashes)

Uploaded Source

Built Distribution

deepbiome-1.0.0-py3-none-any.whl (156.3 kB view hashes)

Uploaded Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page