Gviz

Plotting data and annotation information along genomic coordinates

Bioconductor version: Release (3.17)

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	1.44.0
In Bioconductor since	BioC 2.10 (R-2.15) (11.5 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
Linking To
Suggests	BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr, rmarkdown, testthat
System Requirements
Enhances
URL	https://github.com/ivanek/Gviz
Bug Reports	https://github.com/ivanek/Gviz/issues

Depends On Me	biomvRCNS, chimeraviz, cicero, coMET, cummeRbund, DMRforPairs, methylationArrayAnalysis, Pviz, rnaseqGene
Imports Me	AllelicImbalance, ASpediaFI, ASpli, BindingSiteFinder, 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, STAN, trackViewer, TVTB, uncoverappLib, VariantFiltering
Suggests Me	annmap, 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

Package Archives

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

Source Package	Gviz_1.44.0.tar.gz
Windows Binary	Gviz_1.44.0.zip
macOS Binary (x86_64)	Gviz_1.44.0.tgz
macOS Binary (arm64)	Gviz_1.44.0.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