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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("pcaExplorer")
In most cases, you don't need to download the package archive at all.
pcaExplorer
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Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Bioconductor version: Release (3.5)
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("pcaExplorer")
Documentation
| HTML | R Script | pcaExplorer User Guide |
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | DimensionReduction, GUI, PrincipalComponent, QualityControl, RNASeq, ReportWriting, Software, Visualization |
| Version | 2.2.1 |
| In Bioconductor since | BioC 3.3 (R-3.3) (1.5 years) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | DESeq2, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, genefilter, ggplot2 (>= 2.0.0), d3heatmap, scales, NMF, plyr, topGO, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, ggrepel, DT, shinyAce, threejs, biomaRt, pheatmap, knitr, rmarkdown, tidyr, grDevices, methods |
| LinkingTo | |
| Suggests | testthat, BiocStyle, airway, org.Hs.eg.db |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/federicomarini/pcaExplorer |
| BugReports | https://github.com/federicomarini/pcaExplorer/issues |
| Depends On Me | |
| Imports Me | ideal |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | pcaExplorer_2.2.1.tar.gz |
| Windows Binary | pcaExplorer_2.2.1.zip |
| Mac OS X 10.11 (El Capitan) | pcaExplorer_2.2.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/pcaExplorer |
| Package Short Url | http://bioconductor.org/packages/pcaExplorer/ |
| Package Downloads Report | Download Stats |
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