microbiomeExplorer

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see microbiomeExplorer.

Microbiome Exploration App

DOI: 10.18129/B9.bioc.microbiomeExplorer

Bioconductor version: 3.21

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>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("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")

microbiomeExplorer HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, Clustering, DifferentialExpression, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software, Visualization

Version 1.18.0

In Bioconductor since BioC 3.12 (R-4.0) (5 years)

License MIT + file LICENSE

Depends shiny, magrittr, metagenomeSeq, Biobase

Imports shinyjs (>= 2.0.0), shinydashboard, shinycssloaders, shinyWidgets, rmarkdown (>= 1.9.0), DESeq2, RColorBrewer, dplyr, tidyr, purrr, 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)

System Requirements

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Suggests V8, testthat (>= 2.1.0)

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package microbiomeExplorer_1.18.0.tar.gz

Windows Binary (x86_64) microbiomeExplorer_1.18.0.zip

macOS Binary (x86_64) microbiomeExplorer_1.18.0.tgz

macOS Binary (arm64) microbiomeExplorer_1.18.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/microbiomeExplorer

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/microbiomeExplorer

Bioc Package Browser https://code.bioconductor.org/browse/microbiomeExplorer/

Package Short Url https://bioconductor.org/packages/microbiomeExplorer/

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