MicrobiotaProcess

DOI: 10.18129/B9.bioc.MicrobiotaProcess    

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

Bioconductor version: Release (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>

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

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 1.2.0
In Bioconductor since BioC 3.11 (R-4.0) (0.5 years)
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, randomForest, rlang, tibble, grDevices, stats, utils, coin, ggsignif, scales, Rmisc, DECIPHER, biomformat, yaml, phangorn, patchwork
LinkingTo
Suggests DT, prettydoc, treeio, tidyverse, testthat, knitr, nlme
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_1.2.0.tar.gz
Windows Binary MicrobiotaProcess_1.2.0.zip
macOS 10.13 (High Sierra) MicrobiotaProcess_1.2.0.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

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