Gviz

Plotting data and annotation information along genomic coordinates

Bioconductor version: Development (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>

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   Reference Manual
Text   NEWS

Details

biocViews Microarray, Software, Visualization
Version 1.9.0
In Bioconductor since BioC 2.10 (R-2.15)
License Artistic-2.0
Depends R (>= 2.10.0), methods, grid, BiocGenerics(>= 0.1.4)
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), GenomicFeatures(>= 1.9.7), BSgenome(>= 1.31.5), Biostrings(>= 2.31.8), biovizBase(>= 1.5.7), Rsamtools(>= 1.11.1), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14), GenomicAlignments(>= 0.99.11)
Suggests xtable, BSgenome.Hsapiens.UCSC.hg19, BiocStyle
System Requirements
URL
Depends On Me biomvRCNS, cummeRbund, DMRforPairs
Imports Me GGtools, methyAnalysis, PING, trackViewer
Suggests Me annmap, CNEr, gwascat, interactiveDisplay, QuasR, SplicingGraphs

Package Downloads

Package Source Gviz_1.9.0.tar.gz
Windows Binary Gviz_1.9.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) Gviz_1.9.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

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