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:

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

Please visit https://vallenderlab.github.io/MicrobiomeR/ for extensive documentation of the package.

Citation

If you use MicrobiomeR, please cite the associated Journal of Open Source Software article:

Gilmore RA, Hutchins S, Zhang X, Vallender E. (2019). MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows. Journal of Open Source Software, 4(35), 1299. https://doi.org/10.21105/joss.01299

The same citation is available from R:

citation("MicrobiomeR")

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.