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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")):

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MicrobiomeProfiler")

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

Documentation

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

browseVignettes("MicrobiomeProfiler")
Introduction to MicrobiotaProcess HTML R Script
Reference Manual PDF

Details

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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Depends On Me
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Build Report 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) 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/
Package Downloads Report Download Stats