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 (3.21)

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] (ORCID: )

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

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DimensionReduction, GUI, ImmunoOncology, PrincipalComponent, QualityControl, RNASeq, ReportWriting, ShinyApps, Software, Visualization
Version	3.1.1
In Bioconductor since	BioC 3.3 (R-3.3) (8.5 years)
License	MIT + file LICENSE
Depends
Imports	DESeq2, SummarizedExperiment, mosdef(>= 1.1.0), 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

Suggests	testthat, BiocStyle, markdown, airway, org.Hs.eg.db, htmltools
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	GeDi
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	pcaExplorer_3.1.1.tar.gz
Windows Binary (x86_64)
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
Bioc Package Browser	https://code.bioconductor.org/browse/pcaExplorer/
Package Short Url	https://bioconductor.org/packages/pcaExplorer/
Package Downloads Report	Download Stats