DOI: 10.18129/B9.bioc.MicrobiomeProfiler  

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:



HTML R Script Introduction to MicrobiotaProcess
PDF   Reference Manual


biocViews KEGG, Microbiome, Software, Visualization
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2 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
Suggests rmarkdown, knitr, testthat (>= 3.0.0), prettydoc
URL https://github.com/YuLab-SMU/MicrobiomeProfiler/
BugReports https://github.com/YuLab-SMU/MicrobiomeProfiler/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

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)
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/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: