MicrobiomeProfiler

This is the released version of MicrobiomeProfiler; for the devel version, see MicrobiomeProfiler.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14

An R/shiny package for microbiome functional enrichment analysis

Bioconductor version: Release (3.23)

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 [cre, aut] ORCID: 0000-0002-6485-8781 , Meijun Chen [aut] ORCID: 0000-0003-2486-8106

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

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

Guangchuang Yu, Meijun Chen. MicrobiomeProfiler: An R/shiny package for microbiome functional enrichment analysis. doi:10.18129/B9.bioc.MicrobiomeProfiler, R package version 1.18.1, https://bioconductor.org/packages/MicrobiomeProfiler.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

Introduction to MicrobiotaProcess	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	KEGG, Microbiome, Software, Visualization
Version	1.18.1
In Bioconductor since	BioC 3.14 (R-4.1) (5 years)
License	GPL-2
Depends	R (>= 4.2.0)
Imports	clusterProfiler (>= 4.5.2), enrichit, config, DT, enrichplot, golem, gson, methods, magrittr, shiny (>= 1.6.0), shinyWidgets, shinycustomloader, htmltools, ggplot2, graphics, stats, utils, yulab.utils
System Requirements
URL	https://github.com/YuLab-SMU/MicrobiomeProfiler/ https://yulab-smu.top/contribution-knowledge-mining/
Bug Reports	https://github.com/YuLab-SMU/MicrobiomeProfiler/issues

Suggests	rmarkdown, knitr, testthat (>= 3.0.0), prettydoc
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	MicrobiomeProfiler_1.18.1.tar.gz
Windows Binary (x86_64)	MicrobiomeProfiler_1.18.1.zip
macOS Binary (big-sur-x86_64)	MicrobiomeProfiler_1.18.1.tgz
macOS Binary (sonoma-arm64)	MicrobiomeProfiler_1.18.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MicrobiomeProfiler
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MicrobiomeProfiler
Package Short Url	https://bioconductor.org/packages/MicrobiomeProfiler/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive