source("http://bioconductor.org/biocLite.R")
biocLite("Gviz")

Gviz

Plotting data and annotation information along genomic coordinates

Bioconductor version: 2.13

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.

Author: Florian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Lianoglou, Ge Tan <ge.tan09 at imperial.ac.uk>

Maintainer: Florian Hahne <florian.hahne at novartis.com>

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("Gviz")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Gviz")

 

PDF	R Script	Gviz users guide
PDF		ucsc1.pdf
PDF		ucsc2.pdf
PDF		Reference Manual
Text		NEWS

Details

biocViews	Microarray, Software, Visualization
Version	1.6.0
In Bioconductor since	BioC 2.10 (R-2.15)
License	Artistic-2.0
Depends	R (>= 2.10.0), methods, grid
Imports	IRanges(>= 1.19.5), XVector, rtracklayer(>= 1.15.5), lattice, RColorBrewer, biomaRt(>= 2.11.0), GenomicRanges(>= 1.7.14), AnnotationDbi(>= 1.17.11), Biobase(>= 2.15.3), BiocGenerics(>= 0.1.4), GenomicFeatures(>= 1.9.7), BSgenome(>= 1.25.1), Biostrings(>= 2.25.1), biovizBase(>= 1.5.7), Rsamtools(>= 1.11.1), latticeExtra (>= 0.6-26)
Suggests	xtable, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, biomaRt, rtracklayer
System Requirements
URL
Depends On Me	biomvRCNS, cummeRbund
Imports Me	interactiveDisplay, methyAnalysis, PING
Suggests Me	gwascat, QuasR, SplicingGraphs

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	Gviz_1.6.0.tar.gz
Windows Binary	Gviz_1.6.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	Gviz_1.6.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats