Welcome to the new bioconductor.org!

microbiomeMarker

This is the development version of microbiomeMarker; for the stable release version, see microbiomeMarker.

microbiome biomarker analysis toolkit


Bioconductor version: Development (3.19)

To date, a number of methods have been developed for microbiome marker discovery based on metagenomic profiles, e.g. LEfSe. However, all of these methods have its own advantages and disadvantages, and none of them is considered standard or universal. Moreover, different programs or softwares may be development using different programming languages, even in different operating systems. Here, we have developed an all-in-one R package microbiomeMarker that integrates commonly used differential analysis methods as well as three machine learning-based approaches, including Logistic regression, Random forest, and Support vector machine, to facilitate the identification of microbiome markers.

Author: Yang Cao [aut, cre]

Maintainer: Yang Cao <caoyang.name at gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("microbiomeMarker")

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("microbiomeMarker")
Tools for microbiome marker identification HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, Metagenomics, Microbiome, Software
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.1.0)
Imports dplyr, phyloseq, magrittr, purrr, MASS, utils, ggplot2, tibble, rlang, stats, coin, ggtree, tidytree, methods, IRanges, tidyr, patchwork, ggsignif, metagenomeSeq, DESeq2, edgeR, BiocGenerics, Biostrings, yaml, biomformat, S4Vectors, Biobase, ComplexHeatmap, ANCOMBC, caret, limma, ALDEx2, multtest, plotROC, vegan, pROC, BiocParallel
System Requirements
URL https://github.com/yiluheihei/microbiomeMarker
Bug Reports https://github.com/yiluheihei/microbiomeMarker/issues
See More
Suggests testthat, covr, glmnet, Matrix, kernlab, e1071, ranger, knitr, rmarkdown, BiocStyle, withr
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 microbiomeMarker_1.9.0.tar.gz
Windows Binary microbiomeMarker_1.9.0.zip
macOS Binary (x86_64) microbiomeMarker_1.9.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/microbiomeMarker
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/microbiomeMarker
Bioc Package Browser https://code.bioconductor.org/browse/microbiomeMarker/
Package Short Url https://bioconductor.org/packages/microbiomeMarker/
Package Downloads Report Download Stats