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 (3.0)

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 1.10.1
In Bioconductor since BioC 2.10 (R-2.15)
License Artistic-2.0
Depends R (>= 2.10.0), methods, grid, BiocGenerics(>= 0.11.3), S4Vectors(>= 0.1.0), IRanges(>= 1.99.18), GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.17.20)
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)
Suggests xtable, BSgenome.Hsapiens.UCSC.hg19, BiocStyle
System Requirements
URL
Depends On Me biomvRCNS, cummeRbund, DMRforPairs, Pbase, Pviz
Imports Me AllelicImbalance, GGtools, methyAnalysis, methylPipe, PING, trackViewer
Suggests Me annmap, CNEr, gwascat, interactiveDisplay, QuasR, SplicingGraphs, STAN

Package Archives

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

Package Source Gviz_1.10.1.tar.gz
Windows Binary Gviz_1.10.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) Gviz_1.10.1.tgz
Mac OS X 10.9 (Mavericks) Gviz_1.10.1.tgz
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