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microbiomeExplorer

This is the development version of microbiomeExplorer; for the stable release version, see microbiomeExplorer.

Microbiome Exploration App

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Classification, Clustering, DifferentialExpression, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software, Visualization
Version 1.11.0
In Bioconductor since BioC 3.12 (R-4.0) (3 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)
Linking To
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_1.11.0.tar.gz
Windows Binary microbiomeExplorer_1.11.0.zip (64-bit only)
macOS Binary (x86_64) microbiomeExplorer_1.11.0.tgz
macOS Binary (arm64)
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/
Package Downloads Report Download Stats