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

An R/shiny package for microbiome functional enrichment analysis

Bioconductor version: Development (3.19)

This is an R/shiny package to perform functional enrichment analysis for microbiome data. This package was based on clusterProfiler. Moreover, MicrobiomeProfiler support KEGG enrichment analysis, COG enrichment analysis, Microbe-Disease association enrichment analysis, Metabo-Pathway analysis.

Author: Guangchuang Yu [aut, ths] , Meijun Chen [aut, cre]

Maintainer: Meijun Chen <mjchen1996 at outlook.com>

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


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:

Introduction to MicrobiotaProcess HTML R Script
Reference Manual PDF


biocViews KEGG, Microbiome, Software, Visualization
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-2
Depends R (>= 4.2.0)
Imports clusterProfiler(>= 4.5.2), config, DT, enrichplot, golem, gson, methods, magrittr, shiny (>= 1.6.0), shinyWidgets, shinycustomloader, htmltools, ggplot2, graphics, stats, utils
System Requirements
URL https://github.com/YuLab-SMU/MicrobiomeProfiler/
Bug Reports https://github.com/YuLab-SMU/MicrobiomeProfiler/issues
See More
Suggests rmarkdown, knitr, testthat (>= 3.0.0), prettydoc
Linking To
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MicrobiomeProfiler_1.9.0.tar.gz
Windows Binary MicrobiomeProfiler_1.9.0.zip
macOS Binary (x86_64) MicrobiomeProfiler_1.9.0.tgz
macOS Binary (arm64) MicrobiomeProfiler_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MicrobiomeProfiler
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MicrobiomeProfiler
Bioc Package Browser https://code.bioconductor.org/browse/MicrobiomeProfiler/
Package Short Url https://bioconductor.org/packages/MicrobiomeProfiler/
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