microbiomeExplorer

DOI: 10.18129/B9.bioc.microbiomeExplorer    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see microbiomeExplorer.

Microbiome Exploration App

Bioconductor version: 3.12

The MicrobiomeExplorer R package is designed to facilitate the analysis and visualization of marker-gene survey feature data. It allows a user to perform and visualize typical microbiome analytical workflows either through the command line or an interactive Shiny application included with the package. In addition to applying common analytical workflows the application enables automated analysis report generation.

Author: Joseph Paulson [aut], Janina Reeder [aut, cre], Mo Huang [aut], Genentech [cph, fnd]

Maintainer: Janina Reeder <reederj1 at gene.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("microbiomeExplorer")

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("microbiomeExplorer")

 

HTML	R Script	microbiomeExplorer
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Classification, Clustering, DifferentialExpression, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software, Visualization
Version	1.0.1
In Bioconductor since	BioC 3.12 (R-4.0) (0.5 years)
License	MIT + file LICENSE
Depends	shiny, magrittr, metagenomeSeq, Biobase
Imports	shinyjs, shinydashboard, shinycssloaders, shinyWidgets, rmarkdown (>= 1.9.0), DESeq2, RColorBrewer, dplyr, tidyr, rlang, knitr, readr, DT (>= 0.12.0), biomformat, tools, stringr, vegan, matrixStats, heatmaply, car, broom, limma, reshape2, tibble, forcats, lubridate, methods, plotly (>= 4.9.1)
LinkingTo
Suggests	V8, testthat (>= 2.1.0)
SystemRequirements
Enhances
URL
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	microbiomeExplorer_1.0.1.tar.gz
Windows Binary	microbiomeExplorer_1.0.1.zip
macOS 10.13 (High Sierra)	microbiomeExplorer_1.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/microbiomeExplorer
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/microbiomeExplorer
Package Short Url	https://bioconductor.org/packages/microbiomeExplorer/
Package Downloads Report	Download Stats