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A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Bioconductor version: Release (3.19)

MicrobiotaProcess is an R package for analysis, visualization and biomarker discovery of microbial datasets. It introduces MPSE class, this make it more interoperable with the existing computing ecosystem. Moreover, it introduces a tidy microbiome data structure paradigm and analysis grammar. It provides a wide variety of microbiome data analysis procedures under the unified and common framework (tidy-like framework).

Author: Shuangbin Xu [aut, cre] , Guangchuang Yu [aut, ctb]

Maintainer: Shuangbin Xu <xshuangbin at>

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


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Introduction to MicrobiotaProcess HTML R Script
Reference Manual PDF


biocViews FeatureExtraction, Microbiome, MultipleComparison, Software, Visualization
Version 1.16.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL (>= 3.0)
Depends R (>= 4.0.0)
Imports ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel, vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, patchwork, ggstar, tidyselect, SummarizedExperiment, foreach, treeio(>= 1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table, ggfun (>= 0.1.1)
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Suggests rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, ggupset, ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial, ggpp, BiocManager
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Follow Installation instructions to use this package in your R session.

Source Package MicrobiotaProcess_1.16.0.tar.gz
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macOS Binary (x86_64) MicrobiotaProcess_1.16.0.tgz
macOS Binary (arm64) MicrobiotaProcess_1.16.0.tgz
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