microbiomeExplorer
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see microbiomeExplorer.
Microbiome Exploration App
Bioconductor version: 3.19
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("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
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, Clustering, DifferentialExpression, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software, Visualization |
| Version | 1.14.0 |
| 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 |
See More
| Suggests | V8, testthat (>= 2.1.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | microbiomeExplorer_1.14.0.tar.gz |
| Windows Binary (x86_64) | microbiomeExplorer_1.14.0.zip (64-bit only) |
| macOS Binary (x86_64) | microbiomeExplorer_1.14.0.tgz |
| macOS Binary (arm64) | microbiomeExplorer_1.14.0.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 |