pcaExplorer

DOI: 10.18129/B9.bioc.pcaExplorer  

Interactive Visualization of RNA-seq Data Using a Principal Components Approach

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")

 

HTML	R Script	pcaExplorer User Guide
HTML	R Script	Up and running with pcaExplorer
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DimensionReduction, GUI, ImmunoOncology, PrincipalComponent, QualityControl, RNASeq, ReportWriting, Software, Visualization
Version	2.24.0
In Bioconductor since	BioC 3.3 (R-3.3) (7 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
LinkingTo
Suggests	testthat, BiocStyle, airway, org.Hs.eg.db, htmltools
SystemRequirements
Enhances
URL	https://github.com/federicomarini/pcaExplorer https://federicomarini.github.io/pcaExplorer/
BugReports	https://github.com/federicomarini/pcaExplorer/issues
Depends On Me
Imports Me	ideal
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	pcaExplorer_2.24.0.tar.gz
Windows Binary	pcaExplorer_2.24.0.zip
macOS Binary (x86_64)	pcaExplorer_2.24.0.tgz
macOS Binary (arm64)	pcaExplorer_2.24.0.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