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.