pcaExplorer
This is the development version of pcaExplorer; for the stable release version, see pcaExplorer.
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Bioconductor version: Development (3.21)
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.
Author: Federico Marini [aut, cre] (ORCID:
Maintainer: Federico Marini <marinif at uni-mainz.de>
citation("pcaExplorer")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("pcaExplorer")
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("pcaExplorer")| pcaExplorer User Guide | HTML | R Script |
| Up and running with pcaExplorer | HTML | R Script |
| Reference Manual |
Details
| biocViews | DimensionReduction, GUI, ImmunoOncology, PrincipalComponent, QualityControl, RNASeq, ReportWriting, ShinyApps, Software, Visualization |
| Version | 3.1.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 years) |
| License | MIT + file LICENSE |
| Depends | |
| 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 |
| System Requirements | |
| URL | https://github.com/federicomarini/pcaExplorer https://federicomarini.github.io/pcaExplorer/ |
| Bug Reports | https://github.com/federicomarini/pcaExplorer/issues |
See More
| Suggests | testthat, BiocStyle, markdown, airway, org.Hs.eg.db, htmltools |
| 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 | pcaExplorer_3.1.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/pcaExplorer |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/pcaExplorer |
| Bioc Package Browser | https://code.bioconductor.org/browse/pcaExplorer/ |
| Package Short Url | https://bioconductor.org/packages/pcaExplorer/ |
| Package Downloads Report | Download Stats |