To install this package, start R and enter:
## try http if https is not available
source("https://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:
## try http if https is not available
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")
| R Script | Gviz users guide | |
| 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) |
| Git source | https://github.com/Bioconductor-mirror/Gviz/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/Gviz/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
