Gviz

Plotting data and annotation information along genomic coordinates

Bioconductor version: Release (2.11)

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>

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

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("Gviz")

Documentation

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

Details

biocViews	Microarray, Software, Visualization
Version	1.2.1
In Bioconductor since	BioC 2.10 (R-2.15)
License	Artistic-2.0
Depends	R (>= 2.10.0), methods, grid
Imports	IRanges(>= 1.13.19), 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)
Suggests	xtable, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19
System Requirements
URL
Depends On Me	cummeRbund
Imports Me	methyAnalysis, PING
Suggests Me	gwascat

Package Downloads

Package Source	Gviz_1.2.1.tar.gz
Windows Binary	Gviz_1.2.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard)	Gviz_1.2.1.tgz
Package Downloads Report	Download Stats

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