MicrobiotaProcess

DOI: 10.18129/B9.bioc.MicrobiotaProcess    

This package is for version 3.12 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: 3.12

MicrobiotaProcess is an R package for analysis, visualization and biomarker discovery of microbial datasets. It supports calculating alpha index and provides functions to visualize rarefaction curves. Moreover, it also supports visualizing the abundance of taxonomy of samples. And It also provides functions to perform the PCA, PCoA and hierarchical cluster analysis. In addition, MicrobiotaProcess also provides a method for the biomarker discovery of metagenome or other datasets.

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

Maintainer: Shuangbin Xu <xshuangbin at 163.com>

Installation

To install this package, start R (version "4.0") 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	MicrobiotaProcess: basics analysis using MicrobiotaProcess.
HTML	R Script	MicrobiotaProcess: biomarker discovery using MicrobiotaProcess.
PDF		Reference Manual
Text		NEWS

Details

biocViews	FeatureExtraction, Microbiome, MultipleComparison, Software, Visualization
Version	1.2.2
In Bioconductor since	BioC 3.11 (R-4.0) (1 year)
License	GPL (>= 3.0)
Depends	R (>= 4.0.0)
Imports	ape, plyr, tidyr, ggplot2, phyloseq, magrittr, dplyr, Biostrings, ggrepel, vegan, reshape, zoo, ggtree, tidytree, gtools, MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, Rmisc, patchwork, ggstar
LinkingTo
Suggests	DT, rmarkdown, prettydoc, treeio, tidyverse, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, biomformat, scales, yaml
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_1.2.2.tar.gz
Windows Binary	MicrobiotaProcess_1.2.2.zip
macOS 10.13 (High Sierra)	MicrobiotaProcess_1.2.2.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