pcaExplorer

This package is for version 3.17 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: 3.17

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>

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

Installation

To install this package, start R (version "4.3") 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")

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 2.26.1

In Bioconductor since BioC 3.3 (R-3.3) (8 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

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

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