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Gviz

Plotting data and annotation information along genomic coordinates


Bioconductor version: Release (3.18)

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 [aut], Steffen Durinck [aut], Robert Ivanek [aut, cre] , Arne Mueller [aut], Steve Lianoglou [aut], Ge Tan [aut], Lance Parsons [aut], Shraddha Pai [aut], Thomas McCarthy [ctb], Felix Ernst [ctb], Mike Smith [ctb]

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

Citation (from within R, enter citation("Gviz")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Gviz")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Gviz")
The Gviz User Guide HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Microarray, Sequencing, Software, Visualization
Version 1.46.1
In Bioconductor since BioC 2.10 (R-2.15) (12 years)
License Artistic-2.0
Depends R (>= 4.3), 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), ensembldb(>= 2.11.3), 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), graphics, grDevices, stats, utils
System Requirements
URL https://github.com/ivanek/Gviz
Bug Reports https://github.com/ivanek/Gviz/issues
See More
Suggests BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me biomvRCNS, chimeraviz, cicero, coMET, cummeRbund, DMRforPairs, methylationArrayAnalysis, Pviz, rnaseqGene
Imports Me AllelicImbalance, ASpli, CAGEfightR, comapr, crisprViz, DMRcate, DMRcatedata, ELMER, epimutacions, extraChIPs, GeneStructureTools, GenomicInteractions, maser, mCSEA, MEAL, methylPipe, motifbreakR, OGRE, PING, primirTSS, regutools, RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.RiboMethSeq, SPLINTER, srnadiff, tadar, trackViewer, TVTB, uncoverappLib, VariantFiltering
Suggests Me annmap, BindingSiteFinder, CAGEWorkflow, cellbaseR, chipseqDB, CNEr, CNVRanger, DeepBlueR, ensembldb, fishpond, GenomicRanges, gwascat, interactiveDisplay, InterMineR, Pi, pqsfinder, QuasR, RnBeads, segmenter, Single.mTEC.Transcriptomes, SplicingGraphs, TFutils
Links To Me
Build Report Build Report

Package Archives

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

Source Package Gviz_1.46.1.tar.gz
Windows Binary Gviz_1.46.1.zip (64-bit only)
macOS Binary (x86_64) Gviz_1.46.1.tgz
macOS Binary (arm64) Gviz_1.46.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/Gviz
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Gviz
Bioc Package Browser https://code.bioconductor.org/browse/Gviz/
Package Short Url https://bioconductor.org/packages/Gviz/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive