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

We are currently not on CRAN or Bioconductor:

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

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

• Standardization of data wrangling.
  • Phyloseq for data import.
  • Taxa for the primary data object (Taxmap).
  • Proprietary data formatting and validation.
• Phyloseq inspired filtering fortaxa::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

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