MicrobiomeProfiler
This is the development version of MicrobiomeProfiler; for the stable release version, see MicrobiomeProfiler.
An R/shiny package for microbiome functional enrichment analysis
Bioconductor version: Development (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:
Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>
citation("MicrobiomeProfiler")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 1.13.0 |
| 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, 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
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MicrobiomeProfiler_1.13.0.tar.gz |
| Windows Binary (x86_64) | MicrobiomeProfiler_1.13.0.zip (64-bit only) |
| macOS Binary (x86_64) | MicrobiomeProfiler_1.13.0.tgz |
| macOS Binary (arm64) | MicrobiomeProfiler_1.13.0.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 |