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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 (3.19)

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]

Maintainer: Federico Marini <marinif at uni-mainz.de>

Citation (from within R, enter citation("pcaExplorer")):

Installation

To install this package, start R (version "4.4") 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 PDF
NEWS Text
LICENSE Text

Details

biocViews DimensionReduction, GUI, ImmunoOncology, PrincipalComponent, QualityControl, RNASeq, ReportWriting, ShinyApps, Software, Visualization
Version 2.29.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License MIT + file LICENSE
Depends
Imports DESeq2, SummarizedExperiment, 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
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package pcaExplorer_2.29.0.tar.gz
Windows Binary pcaExplorer_2.29.0.zip
macOS Binary (x86_64) pcaExplorer_2.29.0.tgz
macOS Binary (arm64) pcaExplorer_2.29.0.tgz
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