pcaExplorer
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Bioconductor version: 3.24 · Package version: 3.7.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
This package provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates the whole analysis.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pcaExplorer")Details
| Maintainer | Federico Marini <marinif@uni-mainz.de> |
| Author | Federico Marini [aut, cre] (ORCID: <https://orcid.org/0000-0003-3252-7758>) |
| License | MIT + file LICENSE |
| URL | https://github.com/federicomarini/pcaExplorer, https://federicomarini.github.io/pcaExplorer/ |
| Bug Reports | https://github.com/federicomarini/pcaExplorer/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DimensionReduction, GUI, ImmunoOncology, PrincipalComponent, QualityControl, RNASeq, ReportWriting, ShinyApps, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/pcaExplorer/ |
Citation
From within R, enter citation("pcaExplorer"):
Federico Marini. pcaExplorer: Interactive Visualization of RNA-seq Data Using a Principal Components Approach. doi:10.18129/B9.bioc.pcaExplorer, R package version 3.7.0, https://bioconductor.org/packages/pcaExplorer.
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 | pcaExplorer_3.7.0.tar.gz |
| Windows binary (x86_64) | pcaExplorer_3.7.0.zip |
| macOS binary (arm64) | pcaExplorer_3.7.0.tgz |
| macOS binary (x86_64) | pcaExplorer_3.7.0.tgz |
Dependencies
Imports: DESeq2, SummarizedExperiment, mosdef (>= 1.1.0), GenomicRanges, IRanges, S4Vectors, genefilter, ggplot2 (>= 2.0.0), heatmaply, plotly, scales, NMF, plyr, topGO, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, ggrepel, DT, shinyAce, threejs, biomaRt, pheatmap, knitr, rmarkdown, base64enc, tidyr, grDevices, methods
Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, htmltools