MicrobiomeProfiler

DOI: 10.18129/B9.bioc.MicrobiomeProfiler  

An R/shiny package for microbiome functional enrichment analysis

Bioconductor version: Release (3.18)

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 "4.3") and enter:

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

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")

 

HTML R Script Introduction to MicrobiotaProcess
PDF   Reference Manual

Details

biocViews KEGG, Microbiome, Software, Visualization
Version 1.8.0
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
LinkingTo
Suggests rmarkdown, knitr, testthat (>= 3.0.0), prettydoc
SystemRequirements
Enhances
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_1.8.0.tar.gz
Windows Binary MicrobiomeProfiler_1.8.0.zip
macOS Binary (x86_64) MicrobiomeProfiler_1.8.0.tgz
macOS Binary (arm64) MicrobiomeProfiler_1.8.0.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
Old Source Packages for BioC 3.18 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

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