microbiomeExplorer
Microbiome Exploration App
Bioconductor version: 3.23 · Package version: 1.22.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Classification, Clustering, DifferentialExpression, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/microbiomeExplorer/ |
Citation
From within R, enter citation("microbiomeExplorer"):
Joseph Paulson, Janina Reeder, Mo Huang. microbiomeExplorer: Microbiome Exploration App. doi:10.18129/B9.bioc.microbiomeExplorer, R package version 1.22.0, https://bioconductor.org/packages/microbiomeExplorer.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
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)