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	263
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

Source package

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)