DOI: 10.18129/B9.bioc.microbiomeExplorer  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see microbiomeExplorer.

Microbiome Exploration App

Bioconductor version: 3.16

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 gene.com>

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


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


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HTML R Script microbiomeExplorer
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biocViews Classification, Clustering, DifferentialExpression, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software, Visualization
Version 1.8.0
In Bioconductor since BioC 3.12 (R-4.0) (2.5 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)
Suggests V8, testthat (>= 2.1.0)
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package microbiomeExplorer_1.8.0.tar.gz
Windows Binary microbiomeExplorer_1.8.0.zip
macOS Binary (x86_64) microbiomeExplorer_1.8.0.tgz
macOS Binary (arm64) microbiomeExplorer_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/microbiomeExplorer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/microbiomeExplorer
Bioc Package Browser https://code.bioconductor.org/browse/microbiomeExplorer/
Package Short Url https://bioconductor.org/packages/microbiomeExplorer/
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