Gviz
Plotting data and annotation information along genomic coordinates
Bioconductor version: Release (2.12)
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
| R Script | Gviz users guide | |
| ucsc1.pdf | ||
| ucsc2.pdf | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Microarray, Software, Visualization |
| Version | 1.4.5 |
| 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), Rsamtools(>= 1.11.1) |
| Suggests | xtable, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, biomaRt, rtracklayer |
| System Requirements | |
| URL | |
| Depends On Me | biomvRCNS, cummeRbund |
| Imports Me | methyAnalysis, PING |
| Suggests Me | gwascat, QuasR, SplicingGraphs |
Package Downloads
| Package Source | Gviz_1.4.5.tar.gz |
| Windows Binary | Gviz_1.4.5.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | Gviz_1.4.5.tgz |
| Package Downloads Report | Download Stats |
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