To install this package, start R and enter:
source("http://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: 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>, 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:
source("http://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 | 1.10.11 |
| In Bioconductor since | BioC 2.10 (R-2.15) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10.0), methods, grid, BiocGenerics(>= 0.11.3), S4Vectors(>= 0.1.0), IRanges(>= 1.99.18), GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.17.20) |
| 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) |
| LinkingTo | |
| Suggests | xtable, BSgenome.Hsapiens.UCSC.hg19, BiocStyle |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | biomvRCNS, cummeRbund, DMRforPairs, Pbase, Pviz |
| Imports Me | AllelicImbalance, GGtools, methyAnalysis, methylPipe, PING, trackViewer |
| Suggests Me | annmap, CNEr, gwascat, interactiveDisplay, QuasR, SplicingGraphs, STAN |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | Gviz_1.10.11.tar.gz |
| Windows Binary | Gviz_1.10.11.zip |
| Mac OS X 10.6 (Snow Leopard) | Gviz_1.10.11.tgz |
| Mac OS X 10.9 (Mavericks) | Gviz_1.10.11.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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