microbiomeMarker

DOI: 10.18129/B9.bioc.microbiomeMarker    

microbiome biomarker analysis toolkit

Bioconductor version: Release (3.14)

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 "4.1") and enter:

if (!requireNamespace("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 1.0.1
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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
LinkingTo
Suggests testthat, covr, glmnet, Matrix, kernlab, e1071, ranger, knitr, rmarkdown, BiocStyle
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_1.0.1.tar.gz
Windows Binary microbiomeMarker_1.0.1.zip
macOS 10.13 (High Sierra) microbiomeMarker_1.0.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/microbiomeMarker
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/microbiomeMarker
Package Short Url https://bioconductor.org/packages/microbiomeMarker/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

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