microbiomeExplorer

Microbiome Exploration App

Bioconductor version: 3.23 · Package version: 1.22.0

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.

Installation

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

BiocManager::install("microbiomeExplorer")

Details

Maintainer	Janina Reeder <reederj1@gene.com>
Author	Joseph Paulson [aut], Janina Reeder [aut, cre], Mo Huang [aut], Genentech [cph, fnd]
License	MIT + file LICENSE
Downloads rank	441
Source branch	RELEASE_3_23
biocViews	Classification, Clustering, DifferentialExpression, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software, Visualization

Documentation

Using Microbiome Explorer application to analyze amplicon sequencing data

Download

Follow the installation instructions to use this package in your R session.

Source package	microbiomeExplorer_1.22.0.tar.gz
Windows binary (x86_64)	microbiomeExplorer_1.22.0.zip
macOS binary (arm64)	microbiomeExplorer_1.22.0.tgz
macOS binary (x86_64)	microbiomeExplorer_1.22.0.tgz

Dependencies

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)

Suggests: V8, testthat (>= 2.1.0)