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pcaExplorer
This is thereleased version of pcaExplorer; for the devel version, seepcaExplorer.
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Bioconductor version: Release (3.22)
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: 0000-0003-3252-7758
Maintainer: Federico Marini <marinif at uni-mainz.de>
citation("pcaExplorer")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("pcaExplorer")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DimensionReduction,GUI,ImmunoOncology,PrincipalComponent,QualityControl,RNASeq,ReportWriting,ShinyApps,Software,Visualization |
| Version | 3.4.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (9.5 years) |
| License | MIT + fileLICENSE |
| 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/pcaExplorerhttps://federicomarini.github.io/pcaExplorer/ |
| Bug Reports | https://github.com/federicomarini/pcaExplorer/issues |
See More
| Suggests | testthat,BiocStyle,markdown,airway,org.Hs.eg.db,htmltools |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | pcaExplorer_3.4.0.tar.gz |
| Windows Binary (x86_64) | pcaExplorer_3.4.0.zip |
| macOS Binary (x86_64) | pcaExplorer_3.4.0.tgz |
| macOS Binary (arm64) | pcaExplorer_3.4.0.tgz |
| 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 |