microbiomeMarker
microbiome biomarker analysis toolkit
Bioconductor version: Release (3.17)
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("microbiomeMarker")):
Installation
To install this package, start R (version "4.3") 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")| Tools for microbiome marker identification | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, Metagenomics, Microbiome, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (2 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 |
| Linking To | |
| Suggests | testthat, covr, glmnet, Matrix, kernlab, e1071, ranger, knitr, rmarkdown, BiocStyle, withr |
| System Requirements | |
| Enhances | |
| URL | https://github.com/yiluheihei/microbiomeMarker |
| Bug Reports | https://github.com/yiluheihei/microbiomeMarker/issues |
See More
| 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_1.6.0.tar.gz |
| Windows Binary | microbiomeMarker_1.6.0.zip |
| macOS Binary (x86_64) | microbiomeMarker_1.6.0.tgz |
| macOS Binary (arm64) | microbiomeMarker_1.6.0.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 |