pcaExplorer
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Bioconductor version: Release (3.19)
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("pcaExplorer")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | DimensionReduction, GUI, ImmunoOncology, PrincipalComponent, QualityControl, RNASeq, ReportWriting, ShinyApps, Software, Visualization |
Version | 2.30.0 |
In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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 |
System Requirements | |
URL | https://github.com/federicomarini/pcaExplorer https://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 | ideal |
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_2.30.0.tar.gz |
Windows Binary | pcaExplorer_2.30.0.zip (64-bit only) |
macOS Binary (x86_64) | pcaExplorer_2.30.0.tgz |
macOS Binary (arm64) | pcaExplorer_2.30.0.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 |