microbiomeMarker

DOI: 10.18129/B9.bioc.microbiomeMarker  

microbiome biomarker analysis toolkit

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	Tools for microbiome marker identification
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, Metagenomics, Microbiome, Software
Version	1.4.0
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 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
LinkingTo
Suggests	testthat, covr, glmnet, Matrix, kernlab, e1071, ranger, knitr, rmarkdown, BiocStyle, withr
SystemRequirements
Enhances
URL	https://github.com/yiluheihei/microbiomeMarker
BugReports	https://github.com/yiluheihei/microbiomeMarker/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	microbiomeMarker_1.4.0.tar.gz
Windows Binary	microbiomeMarker_1.4.0.zip
macOS Binary (x86_64)	microbiomeMarker_1.4.0.tgz
macOS Binary (arm64)	microbiomeMarker_1.4.0.tgz
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