MicrobiotaProcess

DOI: 10.18129/B9.bioc.MicrobiotaProcess    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see MicrobiotaProcess.

an R package for analysis, visualization and biomarker discovery of microbiome

Bioconductor version: 3.13

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 analsys procedures under the unified and common framework (tidy-like framework).

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

Maintainer: Shuangbin Xu <xshuangbin at 163.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Introduction to MicrobiotaProcess
PDF		Reference Manual
Text		NEWS

Details

biocViews	FeatureExtraction, Microbiome, MultipleComparison, Software, Visualization
Version	1.4.4
In Bioconductor since	BioC 3.11 (R-4.0) (1.5 years)
License	GPL (>= 3.0)
Depends	R (>= 4.0.0)
Imports	ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel, vegan, zoo, ggtree, tidytree (>= 0.3.5), MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, patchwork, ggstar, tidyselect, SummarizedExperiment, foreach, treeio
LinkingTo
Suggests	rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, picante, plyr, DECIPHER, randomForest, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, corrr, ggupset, ggVennDiagram, gghalves, ggalluvial, forcats, pillar, cli, phyloseq, aplot, ggnewscale, ggside, ggtreeExtra
SystemRequirements
Enhances
URL	https://github.com/YuLab-SMU/MicrobiotaProcess/
BugReports	https://github.com/YuLab-SMU/MicrobiotaProcess/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	MicrobiotaProcess_1.4.4.tar.gz
Windows Binary	MicrobiotaProcess_1.4.4.zip
macOS 10.13 (High Sierra)	MicrobiotaProcess_1.4.4.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MicrobiotaProcess
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MicrobiotaProcess
Package Short Url	https://bioconductor.org/packages/MicrobiotaProcess/
Package Downloads Report	Download Stats