microbiomeExplorer

This is the released version of microbiomeExplorer; for the devel version, see microbiomeExplorer.

Microbiome Exploration App

Bioconductor version: Release (3.20)

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 "4.4") 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


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	1.16.0
In Bioconductor since	BioC 3.12 (R-4.0) (4 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
URL

Suggests	V8, testthat (>= 2.1.0)
Linking To
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Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)	microbiomeExplorer_1.16.0.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/
Package Downloads Report	Download Stats