MicrobiotaProcess

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see MicrobiotaProcess.

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

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0003-3513-5362 , Guangchuang Yu [aut, ctb] ORCID iD ORCID: 0000-0002-6485-8781

Maintainer: Shuangbin Xu <xshuangbin at 163.com>

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

Installation

To install this package, start R (version "4.5") and enter:


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

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("MicrobiotaProcess")

Introduction to MicrobiotaProcess HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews FeatureExtraction, Microbiome, MultipleComparison, Software, Visualization

Version 1.20.2

In Bioconductor since BioC 3.11 (R-4.0) (5.5 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)

System Requirements

URL https://github.com/YuLab-SMU/MicrobiotaProcess/

Bug Reports https://github.com/YuLab-SMU/MicrobiotaProcess/issues

Suggests rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, ggupset, ggVennDiagram, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial, ggpp, BiocManager

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Package Archives

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

Source Package MicrobiotaProcess_1.20.2.tar.gz

Windows Binary (x86_64) MicrobiotaProcess_1.20.1.zip

macOS Binary (x86_64) MicrobiotaProcess_1.20.2.tgz

macOS Binary (arm64) MicrobiotaProcess_1.20.2.tgz

Source Repository git clone https://git.bioconductor.org/packages/MicrobiotaProcess

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MicrobiotaProcess

Bioc Package Browser https://code.bioconductor.org/browse/MicrobiotaProcess/

Package Short Url https://bioconductor.org/packages/MicrobiotaProcess/

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Old Source Packages for BioC 3.21 Source Archive