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 (3.17)

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 "4.3") 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")

 

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

Details

biocViews	DimensionReduction, GUI, ImmunoOncology, PrincipalComponent, QualityControl, RNASeq, ReportWriting, Software, Visualization
Version	2.25.0
In Bioconductor since	BioC 3.3 (R-3.3) (6.5 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_2.25.0.tar.gz
Windows Binary
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
Package Short Url	https://bioconductor.org/packages/pcaExplorer/
Package Downloads Report	Download Stats