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Bioconductor - MicrobiomeProfiler

MicrobiomeProfiler

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

An R/shiny package for microbiome functional enrichment analysis

Bioconductor version: Release (3.21)

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")): Installation

To install this package, start R (version "4.5") 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")
Details biocViews KEGG, Microbiome, Software, Visualization Version 1.14.0 In Bioconductor since BioC 3.14 (R-4.1) (3.5 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, 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 See More Package Archives

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

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