Gviz

DOI: 10.18129/B9.bioc.Gviz    

Plotting data and annotation information along genomic coordinates

Bioconductor version: Release (3.6)

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>, Shraddha Pai <shraddha.pai at utoronto.ca>

Maintainer: Robert Ivanek <robert.ivanek at unibas.ch>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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	1.22.3
In Bioconductor since	BioC 2.10 (R-2.15) (6 years)
License	Artistic-2.0
Depends	R (>= 2.10.0), methods, S4Vectors(>= 0.9.25), 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	biomvRCNS, chimeraviz, coMET, cummeRbund, DMRforPairs, Pbase, Pviz
Imports Me	AllelicImbalance, ASpli, DMRcate, ELMER, GenomicInteractions, GGtools, gwascat, InPAS, MEAL, methyAnalysis, methylPipe, motifbreakR, Pi, PING, SPLINTER, STAN, trackViewer, TVTB, VariantFiltering
Suggests Me	annmap, cellbaseR, CNEr, DeepBlueR, ensembldb, GenomicRanges, interactiveDisplay, InterMineR, pqsfinder, QuasR, RnBeads, Single.mTEC.Transcriptomes, SplicingGraphs
Build Report

Package Archives

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

Source Package	Gviz_1.22.3.tar.gz
Windows Binary	Gviz_1.22.3.zip
Mac OS X 10.11 (El Capitan)	Gviz_1.22.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Gviz
Package Short Url	http://bioconductor.org/packages/Gviz/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive