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MicrobiomeR

MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows - Published in JOSS (2019)

https://github.com/vallenderlab/microbiomer

Science Score: 100.0%

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 4 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ✓
    Committers with academic emails
    1 of 5 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

alpha-diversity beta-diversity bioinformatics color-palette comprehensive metacoder metagenomics microbial-genomics microbiology microbiome microbiome-analysis pcoa permanova phyloseq r rstats visualization
Last synced: 4 months ago · JSON representation ·

Repository

A comprehensive and customizable R package for microbiome analysis.

Basic Info
Statistics
  • Stars: 23
  • Watchers: 3
  • Forks: 4
  • Open Issues: 16
  • Releases: 8
Topics
alpha-diversity beta-diversity bioinformatics color-palette comprehensive metacoder metagenomics microbial-genomics microbiology microbiome microbiome-analysis pcoa permanova phyloseq r rstats visualization
Created over 7 years ago · Last pushed 5 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

Build Status lifecycle Coverage status DOI

MicrobiomeR

An R package for microbiome analysis that incorporates phyloseq, metacoder, taxa, and microbiome in order to standardize and simplify common microbiome workflows.

Installation

We are currently not on CRAN or Bioconductor:

r library(devtools) # Load the devtools package install_github("vallenderlab/MicrobiomeR") # Install the package

Please visit https://microbiomer.vallenderlab.org/ for extensive documentation of the package.

Workflow Features

  • Standardization of data wrangling.
    • Phyloseq for data import.
    • Taxa for the primary data object (Taxmap).
    • Proprietary data formatting and validation.
  • Phyloseq inspired filtering for taxa::taxmap objects.
    • Metacoder/taxa for mainstream filtering.
    • Proprietary basic filtering for samples, taxonomies, and OTUs.
    • Proprietary advanced filtering (phyloseq-style).
    • Other Proprietary filtering functions for observation data.
  • Metacoder enabled statistical analysis functions.
  • Various visualization options.
    • Output Directories
    • Color Palettes
    • Heat Trees
    • Correlation Plots
    • Stacked Bar Plot
    • Alpha Diversity Plot
    • Ordination Plot

Contributing to MicrobiomeR

  • Our code style is based on Google's R style developed by Hadley Wickham.
  • Please note that the MicrobiomeR project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
  • View our contributing documentation for more details.

Owner

  • Name: Vallender Lab
  • Login: vallenderlab
  • Kind: organization
  • Email: vallenderlab@ummc.onmicrosoft.com

Data and software created and/or published by the Vallender Lab

JOSS Publication

MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows
Published
March 31, 2019
DOI
Volume 4, Issue 35, Page 1299
Authors
Robert A. Gilmore ORCID
Department of Neurobiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
Shaurita Hutchins ORCID
Department of Neurobiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
Xiao Zhang ORCID
Department of Neurobiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
Eric Vallender ORCID
Department of Neurobiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
Editor
Lorena Pantano ORCID
Tags
bioinformatics microbiome taxonomy
View PDF Review Thread Software Archive

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use MicrobiomeR, please cite the following publication."
title: "MicrobiomeR"
version: 1.0.0
doi: 10.21105/joss.01299
date-released: 2019-03-31
url: "https://doi.org/10.21105/joss.01299"
authors:
  - family-names: "Gilmore"
    given-names: "Robert A."
    orcid: "https://orcid.org/0000-0001-8096-0180"
  - family-names: "Hutchins"
    given-names: "Shaurita"
    orcid: "https://orcid.org/0000-0002-7687-0059"
  - family-names: "Zhang"
    given-names: "Xiao"
    orcid: "https://orcid.org/0000-0001-5710-6496"
  - family-names: "Vallender"
    given-names: "Eric"
    orcid: "https://orcid.org/0000-0003-3506-0540"

preferred-citation:
  type: article
  title: "MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows"
  authors:
    - family-names: "Gilmore"
      given-names: "Robert A."
      orcid: "https://orcid.org/0000-0001-8096-0180"
    - family-names: "Hutchins"
      given-names: "Shaurita"
      orcid: "https://orcid.org/0000-0002-7687-0059"
    - family-names: "Zhang"
      given-names: "Xiao"
      orcid: "https://orcid.org/0000-0001-5710-6496"
    - family-names: "Vallender"
      given-names: "Eric"
      orcid: "https://orcid.org/0000-0003-3506-0540"
  journal: "Journal of Open Source Software"
  volume: 4
  issue: 35
  start: 1299
  doi: "10.21105/joss.01299"
  year: 2019
  month: 3
  url: "https://doi.org/10.21105/joss.01299"

GitHub Events

Total
  • Issues event: 1
  • Watch event: 3
  • Issue comment event: 2
  • Push event: 1
  • Pull request event: 2
Last Year
  • Issues event: 1
  • Watch event: 3
  • Issue comment event: 2
  • Push event: 1
  • Pull request event: 2

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 844
  • Total Committers: 5
  • Avg Commits per committer: 168.8
  • Development Distribution Score (DDS): 0.341
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
grabear r****7@g****m 556
sdhutchins m****s@g****m 273
sdhutchins s****s@o****m 10
Shaurita Hutchins s****2@u****u 3
grabear r****e@g****m 2
Committer Domains (Top 20 + Academic)
umc.edu: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 42
  • Total pull requests: 59
  • Average time to close issues: 2 months
  • Average time to close pull requests: about 21 hours
  • Total issue authors: 8
  • Total pull request authors: 2
  • Average comments per issue: 4.36
  • Average comments per pull request: 1.46
  • Merged pull requests: 54
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • grabear (26)
  • sdhutchins (10)
  • avportal (1)
  • tulsijoishy (1)
  • sielerjm (1)
  • tboonf (1)
  • cafferychen777 (1)
  • ghost (1)
Pull Request Authors
  • grabear (31)
  • sdhutchins (29)
Top Labels
Issue Labels
Status: In Progress :construction: :construction: (12) Type: Discussion :speech_balloon: (11) Type: Enhancement :heart: (10) Priority: Critical :fire::fire::fire::fire: (9) Type: Bug :beetle: :beetle: :beetle: :beetle: (7) Priority: Medium :fire::fire: (6) Type: Documentation :page_facing_up: (6) Status: Review Needed :eye: :eye: (5) Type: Maintenance :wrench: (5) Status: Completed :checkered_flag::checkered_flag: (5) Priority: High :fire::fire::fire: (4) Status: Available :seat: (4) Status: On Hold :zzz: :zzz: (4) Epic (3) Type: Feature 🎥 (3) Type: Question :question: (2) Status: Help Wanted :sos: (2) Priority: Low :fire: (2) :pushpin: Status: Pending :pushpin: (1) Type: Duplicate :memo::memo::memo: (1) :skull: Status: Abandoned :skull: (1) Status: Revision Needed :hammer_and_wrench: (1) Beginner Friendly (1)
Pull Request Labels
Type: Maintenance :wrench: (9) Status: Review Needed :eye: :eye: (7) Priority: Critical :fire::fire::fire::fire: (6) Type: Documentation :page_facing_up: (6) Type: Feature 🎥 (5) Type: Enhancement :heart: (4) Priority: High :fire::fire::fire: (4) Type: Bug :beetle: :beetle: :beetle: :beetle: (3) Priority: Medium :fire::fire: (3) Status: In Progress :construction: :construction: (3) Epic (1) Status: Completed :checkered_flag::checkered_flag: (1) Priority: Low :fire: (1)