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This is the development version of microbiomeExplorer; for the stable release version, see microbiomeExplorer.

Microbiome Exploration App

Bioconductor version: Development (3.20)

The MicrobiomeExplorer R package is designed to facilitate the analysis and visualization of marker-gene survey feature data. It allows a user to perform and visualize typical microbiome analytical workflows either through the command line or an interactive Shiny application included with the package. In addition to applying common analytical workflows the application enables automated analysis report generation.

Author: Joseph Paulson [aut], Janina Reeder [aut, cre], Mo Huang [aut], Genentech [cph, fnd]

Maintainer: Janina Reeder <reederj1 at>

Citation (from within R, enter citation("microbiomeExplorer")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

microbiomeExplorer HTML R Script
Reference Manual PDF


biocViews Classification, Clustering, DifferentialExpression, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software, Visualization
Version 1.15.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License MIT + file LICENSE
Depends shiny, magrittr, metagenomeSeq, Biobase
Imports shinyjs (>= 2.0.0), shinydashboard, shinycssloaders, shinyWidgets, rmarkdown (>= 1.9.0), DESeq2, RColorBrewer, dplyr, tidyr, purrr, rlang, knitr, readr, DT (>= 0.12.0), biomformat, tools, stringr, vegan, matrixStats, heatmaply, car, broom, limma, reshape2, tibble, forcats, lubridate, methods, plotly (>= 4.9.1)
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Suggests V8, testthat (>= 2.1.0)
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Follow Installation instructions to use this package in your R session.

Source Package microbiomeExplorer_1.15.0.tar.gz
Windows Binary
macOS Binary (x86_64) microbiomeExplorer_1.15.0.tgz
macOS Binary (arm64) microbiomeExplorer_1.15.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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