To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("pcaExplorer")

In most cases, you don't need to download the package archive at all.

pcaExplorer

This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see pcaExplorer.

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

Bioconductor version: 3.4

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("pcaExplorer")

Documentation

HTML	R Script	pcaExplorer User Guide
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DimensionReduction, GUI, PrincipalComponent, QualityControl, RNASeq, ReportWriting, Software, Visualization
Version	2.0.0
In Bioconductor since	BioC 3.3 (R-3.3) (1 year)
License	MIT + file LICENSE
Depends
Imports	DESeq2, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, genefilter, ggplot2 (>= 2.0.0), d3heatmap, scales, NMF, plyr, topGO, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, ggrepel, DT, shinyAce, threejs, biomaRt, pheatmap, knitr, rmarkdown, tidyr, grDevices, methods
LinkingTo
Suggests	testthat, BiocStyle, airway, org.Hs.eg.db
SystemRequirements
Enhances
URL	https://github.com/federicomarini/pcaExplorer
BugReports	https://github.com/federicomarini/pcaExplorer/issues
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source	pcaExplorer_2.0.0.tar.gz
Windows Binary	pcaExplorer_2.0.0.zip
Mac OS X 10.9 (Mavericks)	pcaExplorer_2.0.0.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/pcaExplorer/tree/release-3.4
Package Short Url	http://bioconductor.org/packages/pcaExplorer/
Package Downloads Report	Download Stats

Documentation »

Bioconductor

Package vignettes and manuals.
Workflows for learning and use.
Course and conference material.
Videos.
Community resources and tutorials.

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Support site - for questions about Bioconductor packages
Bioc-devel mailing list - for package developers