MicrobiomeProfiler

DOI: 10.18129/B9.bioc.MicrobiomeProfiler  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see MicrobiomeProfiler.

An R/shiny package for microbiome functional enrichment analysis

Bioconductor version: 3.17

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

Maintainer: Meijun Chen <mjchen1996 at outlook.com>

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	1.6.1
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, prettydoc, testthat (>= 3.0.0)
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_1.6.1.tar.gz
Windows Binary	MicrobiomeProfiler_1.6.1.zip
macOS Binary (x86_64)	MicrobiomeProfiler_1.6.1.tgz
macOS Binary (arm64)	MicrobiomeProfiler_1.6.1.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