MicrobiomeProfiler
An R/shiny package for microbiome functional enrichment analysis
Bioconductor version: Release (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("MicrobiomeProfiler")
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Installation
To install this package, start R (version "4.4") 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 |
Details
biocViews | KEGG, Microbiome, Software, Visualization |
Version | 1.10.0 |
In Bioconductor since | BioC 3.14 (R-4.1) (3 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 | |
Enhances | |
Depends On Me | |
Imports 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_1.10.0.tar.gz |
Windows Binary | MicrobiomeProfiler_1.10.0.zip (64-bit only) |
macOS Binary (x86_64) | MicrobiomeProfiler_1.10.0.tgz |
macOS Binary (arm64) | MicrobiomeProfiler_1.10.0.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 |