pcaExplorer

DOI: 10.18129/B9.bioc.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 (3.11)

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 "4.0") and enter:

if (!requireNamespace("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")

 

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 2.13.0
In Bioconductor since BioC 3.3 (R-3.3) (3.5 years)
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, 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_2.13.0.tar.gz
Windows Binary pcaExplorer_2.13.0.zip
Mac OS X 10.11 (El Capitan) pcaExplorer_2.13.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pcaExplorer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pcaExplorer
Package Short Url https://bioconductor.org/packages/pcaExplorer/
Package Downloads Report Download Stats

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