To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

Gviz

 

Plotting data and annotation information along genomic coordinates

Bioconductor version: Release (3.1)

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>, Lance Parsons <lparsons at princeton.edu>

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

Citation (from within R, enter citation("Gviz")):

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   Reference Manual
Text   NEWS

Details

biocViews Microarray, Software, Visualization
Version 1.12.1
In Bioconductor since BioC 2.10 (R-2.15) (3.5 years)
License Artistic-2.0
Depends R (>= 2.10.0), methods, S4Vectors(>= 0.1.0), IRanges(>= 1.99.18), GenomicRanges(>= 1.17.20), grid
Imports XVector(>= 0.5.7), rtracklayer(>= 1.25.13), lattice, RColorBrewer, biomaRt(>= 2.11.0), AnnotationDbi(>= 1.27.5), Biobase(>= 2.15.3), GenomicFeatures(>= 1.17.22), BSgenome(>= 1.33.1), Biostrings(>= 2.33.11), biovizBase(>= 1.13.8), Rsamtools(>= 1.17.28), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14), GenomicAlignments(>= 1.1.16), GenomeInfoDb(>= 1.1.3), BiocGenerics(>= 0.11.3), digest (>= 0.6.8)
LinkingTo
Suggests xtable, BSgenome.Hsapiens.UCSC.hg19, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me AllelicImbalance, biomvRCNS, coMET, cummeRbund, DMRforPairs, Pbase, Pviz
Imports Me AllelicImbalance, GGtools, gwascat, InPAS, methyAnalysis, methylPipe, PING, trackViewer, VariantFiltering
Suggests Me annmap, CNEr, interactiveDisplay, QuasR, RnBeads, SplicingGraphs, STAN
Build Report  

Package Archives

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

Package Source Gviz_1.12.1.tar.gz
Windows Binary Gviz_1.12.1.zip
Mac OS X 10.6 (Snow Leopard) Gviz_1.12.1.tgz
Mac OS X 10.9 (Mavericks) Gviz_1.12.1.tgz
Subversion source (username/password: readonly)
GitHub source https://github.com/Bioconductor-mirror/Gviz/tree/release-3.1
Package Short Url http://bioconductor.org/packages/Gviz/
Package Downloads Report Download Stats

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