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Open Source Science

https://github.com/biocore/birdman

Bayesian Inferential Regression for Differential Microbiome Analysis

https://github.com/biocore/birdman

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.3%) to scientific vocabulary

Keywords

bayesian-inference bioinformatics microbiome python regression stan
Last synced: 5 months ago · JSON representation

Repository

Bayesian Inferential Regression for Differential Microbiome Analysis

Basic Info
  • Host: GitHub
  • Owner: biocore
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 8.09 MB
Statistics
  • Stars: 22
  • Watchers: 4
  • Forks: 5
  • Open Issues: 20
  • Releases: 6
Topics
bayesian-inference bioinformatics microbiome python regression stan
Created over 5 years ago · Last pushed about 2 years ago
Metadata Files
Readme License

README.md

BIRDMAn

GitHub Actions CI Documentation Status PyPI DOI

Bayesian Inferential Regression for Differential Microbiome Analysis (BIRDMAn) is a framework for performing differential abundance analysis through Bayesian inference.

See the documentation for details on usage.

For an example of running BIRDMAn - see this Google Colab notebook.

Installation

Currently BIRDMAn requires Python 3.8 or higher.

We recommend using mamba for installation of dependencies.

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

Owner

  • Name: biocore
  • Login: biocore
  • Kind: organization
  • Location: Cyberspace

Collaboratively developed bioinformatics software.

GitHub Events

Total
  • Issues event: 1
  • Issue comment event: 2
Last Year
  • Issues event: 1
  • Issue comment event: 2

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 223
  • Total Committers: 3
  • Avg Commits per committer: 74.333
  • Development Distribution Score (DDS): 0.018
Top Committers
Name Email Commits
Gibraan Rahman g****n@e****u 219
yangchen2 y****9@g****m 3
Yang Chen 6****2@u****m 1
Committer Domains (Top 20 + Academic)
eng.ucsd.edu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 48
  • Total pull requests: 52
  • Average time to close issues: 4 months
  • Average time to close pull requests: 5 days
  • Total issue authors: 9
  • Total pull request authors: 3
  • Average comments per issue: 1.21
  • Average comments per pull request: 0.62
  • Merged pull requests: 47
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • gibsramen (25)
  • mortonjt (12)
  • jolespin (3)
  • PaulaEterovick (2)
  • yangchen2 (1)
  • mestaki (1)
  • akhilkommala (1)
  • jindongmin (1)
  • liucong-epi (1)
Pull Request Authors
  • gibsramen (47)
  • yangchen2 (3)
  • mortonjt (2)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

setup.py pypi
  • arviz >=0.11.3
  • biom-format *
  • cmdstanpy >=1.0.1
  • matplotlib *
  • numpy *
  • pandas *
  • patsy *
  • xarray *
.github/workflows/main.yml actions
  • actions/checkout v2 composite
  • conda-incubator/setup-miniconda v2 composite
environment.yml conda
  • arviz
  • biom-format
  • cmdstanpy
  • docutils 0.16
  • numpy
  • pandas
  • patsy
  • python 3.7.*
  • python-language-server
  • xarray