MicrobiotaProcess

DOI: 10.18129/B9.bioc.MicrobiotaProcess    

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

Bioconductor version: Release (3.16)

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 163.com>

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

Installation

To install this package, start R (version "4.2") 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")

 

HTML R Script Introduction to MicrobiotaProcess
PDF   Reference Manual
Text   NEWS

Details

biocViews FeatureExtraction, Microbiome, MultipleComparison, Software, Visualization
Version 1.10.2
In Bioconductor since BioC 3.11 (R-4.0) (2.5 years)
License GPL (>= 3.0)
Depends R (>= 4.0.0)
Imports ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel, vegan, zoo, ggtree, tidytree (>= 0.3.9), MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, patchwork, ggstar, tidyselect, SummarizedExperiment, foreach, treeio(>= 1.17.2), pillar, plyr, dtplyr, ggtreeExtra, data.table
LinkingTo
Suggests rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, corrr, ggupset, ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, cli, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial
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_1.10.2.tar.gz
Windows Binary MicrobiotaProcess_1.10.2.zip
macOS Binary (x86_64) MicrobiotaProcess_1.10.2.tgz
macOS Binary (arm64)
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
Old Source Packages for BioC 3.16 Source Archive

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