https://github.com/biocore/birdman

Bayesian Inferential Regression for Differential Microbiome Analysis
https://github.com/biocore/birdman

bayesian-inference bioinformatics microbiome python regression stan

Last synced: about 1 year ago
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Bayesian Inferential Regression for Differential Microbiome Analysis

• Host: GitHub
• URL: https://github.com/biocore/birdman
• Owner: biocore
• License: bsd-3-clause
• Created: 2020-11-11T17:48:45.000Z (over 5 years ago)
• Default Branch: main
• Last Pushed: 2023-12-19T01:30:04.000Z (over 2 years ago)
• Last Synced: 2025-04-11T21:40:30.600Z (about 1 year ago)
• Topics: bayesian-inference, bioinformatics, microbiome, python, regression, stan
• Language: Python
• Homepage:
• Size: 8.09 MB
• Stars: 22
• Watchers: 4
• Forks: 5
• Open Issues: 20
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# BIRDMAn

[![GitHub Actions CI](https://github.com/biocore/birdman/workflows/BIRDMAn%20CI/badge.svg)](https://github.com/biocore/BIRDMAn/actions)

[![Documentation Status](https://readthedocs.org/projects/birdman/badge/?version=latest)](https://birdman.readthedocs.io/en/latest/?badge=latest)

[![PyPI](https://img.shields.io/pypi/v/birdman.svg)](https://pypi.org/project/birdman)

[![DOI](https://zenodo.org/badge/312046610.svg)](https://zenodo.org/badge/latestdoi/312046610)

**B**ayesian **I**nferential **R**egression for **D**ifferential **M**icrobiome **An**alysis (**BIRDMAn**) is a framework for performing differential abundance analysis through Bayesian inference.

See the [documentation](https://birdman.readthedocs.io/en/latest/?badge=latest) for details on usage.

For an example of running BIRDMAn - see this [Google Colab notebook](https://colab.research.google.com/drive/1zT4eIgiz0Jl5TVmttE3gwWnrhNlPeYDc?usp=sharing).

## Installation

Currently BIRDMAn requires Python 3.8 or higher.

We recommend using [mamba](https://github.com/mamba-org/mamba) for installation of dependencies.

```bash

mamba install -c conda-forge biom-format patsy xarray arviz cmdstanpy

pip install birdman

```