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Microbiome.jl and BiobakeryUtils.jl - Julia packages for working with microbial community data

Microbiome.jl and BiobakeryUtils.jl - Julia packages for working with microbial community data - Published in JOSS (2021)

https://github.com/ecojulia/microbiome.jl

Science Score: 98.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

biology ecology julia-language microbiome

Keywords from Contributors

fluxes graphics standardization literate-programming scientific-reports
Last synced: 6 months ago · JSON representation ·

Repository

For analysis of microbiome and microbial community data

Basic Info
  • Host: GitHub
  • Owner: EcoJulia
  • License: other
  • Language: Julia
  • Default Branch: main
  • Homepage:
  • Size: 2.47 MB
Statistics
  • Stars: 48
  • Watchers: 8
  • Forks: 10
  • Open Issues: 9
  • Releases: 29
Topics
biology ecology julia-language microbiome
Created over 8 years ago · Last pushed about 2 years ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

Microbiome.jl logo

status EcoJulia maintainer: kescobo

Latest Release

Latest Release

Docs stable License Project Status: Active – The project has reached a stable, usable state and is being actively developed.

Development Status

Docs dev CI codecov

Description

Microbiome.jl is a package for manipulating and analyzing microbiome and microbial community data.

Installation

To use the latest version of Microbiome.jl, you must be on julia v1.6 or greater.

Install Microbiome.jl from the Julia REPL:

```julia julia> using Pkg

julia> pkg"add Microbiome" ```

If you are interested in the cutting edge of the development, please check out the master branch to try new features before release.

julia julia> pkg"add Microbiome#main"

Companion Packages

  • You might also be interested in some functionality provided by BiobakeryUtils.jl.
  • Microbiome.jl uses EcoBase under the hood for many of its types and methods.
  • Microbiome.jl has a Tables.jl interface, so you can convert CommunityProfiles to any Tables.jl-compatible sink.
    • CommunityProfile is not yet a sink itself

Owner

  • Name: EcoJulia
  • Login: EcoJulia
  • Kind: organization

JOSS Publication

Microbiome.jl and BiobakeryUtils.jl - Julia packages for working with microbial community data
Published
November 17, 2021
DOI
Volume 6, Issue 67, Page 3876
Authors
Kevin S. Bonham
Department of Biological Sciences, Wellesley College
Annelle Abatoni Kayisire
Department of Biological Sciences, Wellesley College
Anika S. Luo
Department of Biological Sciences, Wellesley College
Vanja Klepac-Ceraj
Department of Biological Sciences, Wellesley College
Editor
Will Rowe ORCID
Tags
julia biology microbiome microbial communities
View PDF Review Thread Software Archive

Citation (CITATION.bib) 

% If you use this package in your research, please cite
@article{bonhamMicrobiomeJlBiobakeryUtils2021,
  title = {Microbiome.Jl and {{BiobakeryUtils}}.Jl - {{Julia}} Packages for Working with Microbial Community Data},
  author = {Bonham, Kevin and Kayisire, Annelle and Luo, Anika and {Klepac-Ceraj}, Vanja},
  year = {2021},
  month = nov,
  journal = {J. Open Source Softw.},
  volume = {6},
  number = {67},
  pages = {3876},
  publisher = {{The Open Journal}},
  issn = {2475-9066},
  doi = {10.21105/joss.03876},
  copyright = {http://creativecommons.org/licenses/by/4.0/}
}

GitHub Events

Total
  • Watch event: 2
Last Year
  • Watch event: 2

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 272
  • Total Committers: 10
  • Avg Commits per committer: 27.2
  • Development Distribution Score (DDS): 0.081
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Kevin Bonham k****m@g****m 250
Ben J. Ward w****0@g****m 5
github-actions[bot] 4****] 4
Ben J. Ward b****d@p****m 4
anikaluo 6****o 3
Annelle Abatoni Kayisire 6****i 2
femtocleaner[bot] f****] 1
Parker Knight p****t@g****m 1
Denis Barucic b****d@g****m 1
Kevin Bonham k****n@b****h 1
Committer Domains (Top 20 + Academic)
bonham.ch: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 39
  • Total pull requests: 65
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 3 days
  • Total issue authors: 7
  • Total pull request authors: 7
  • Average comments per issue: 1.62
  • Average comments per pull request: 0.46
  • Merged pull requests: 59
  • Bot issues: 0
  • Bot pull requests: 8
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 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
  • kescobo (25)
  • anikaluo (4)
  • aguang (4)
  • vanjakle (2)
  • EvoArt (2)
  • adRn-s (1)
  • JuliaTagBot (1)
Pull Request Authors
  • kescobo (47)
  • github-actions[bot] (8)
  • anikaluo (4)
  • annelle-abatoni (3)
  • barucden (1)
  • pknight24 (1)
  • SabrinaJaye (1)
Top Labels
Issue Labels
enhancement (13) docs (8) Interop (4) bug (3) compat (2) ci (1) I/O (1) help wanted (1)
Pull Request Labels
enhancement (9) docs (9) compat (2) ci (2) I/O (1) bug (1) release (1)

Packages

  • Total packages: 1
  • Total downloads:
    • julia 5 total
  • Total dependent packages: 2
  • Total dependent repositories: 4
  • Total versions: 26
juliahub.com: Microbiome

For analysis of microbiome and microbial community data

  • Versions: 26
  • Dependent Packages: 2
  • Dependent Repositories: 4
  • Downloads: 5 Total
Rankings
Dependent repos count: 5.6%
Average: 12.3%
Forks count: 13.3%
Stargazers count: 14.7%
Dependent packages count: 15.6%
Last synced: 6 months ago

Dependencies

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.github/workflows/docs.yml actions
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  • codecov/codecov-action v2 composite
  • julia-actions/julia-buildpkg latest composite
  • julia-actions/julia-docdeploy latest composite
  • julia-actions/julia-processcoverage v1 composite
.github/workflows/downstream.yml actions
  • actions/checkout v2 composite
  • julia-actions/julia-buildpkg latest composite
  • julia-actions/setup-julia v1 composite