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pcaExplorer

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

Bioconductor version: 3.23 · Package version: 3.6.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("pcaExplorer")

Details

MaintainerFederico Marini <marinif@uni-mainz.de>
AuthorFederico Marini [aut, cre] (ORCID: <https://orcid.org/0000-0003-3252-7758>)
LicenseMIT + file LICENSE
URLhttps://github.com/federicomarini/pcaExplorer, https://federicomarini.github.io/pcaExplorer/
Bug Reportshttps://github.com/federicomarini/pcaExplorer/issues
Downloads rank591
Source branchRELEASE_3_23
biocViewsDimensionReduction, GUI, ImmunoOncology, PrincipalComponent, QualityControl, RNASeq, ReportWriting, ShinyApps, Software, Visualization

Documentation

Download

Dependencies

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

Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, htmltools