DOI: 10.18129/B9.bioc.microbiomeMarker  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see microbiomeMarker.

microbiome biomarker analysis toolkit

Bioconductor version: 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>

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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
Suggests testthat, covr, glmnet, Matrix, kernlab, e1071, ranger, knitr, rmarkdown, BiocStyle, withr
URL https://github.com/yiluheihei/microbiomeMarker
BugReports https://github.com/yiluheihei/microbiomeMarker/issues
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Source Package microbiomeMarker_1.4.0.tar.gz
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