Gviz

DOI: 10.18129/B9.bioc.Gviz  

Plotting data and annotation information along genomic coordinates

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	The Gviz User Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	Microarray, Sequencing, Software, Visualization
Version	1.42.1
In Bioconductor since	BioC 2.10 (R-2.15) (11 years)
License	Artistic-2.0
Depends	R (>= 4.2), 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
LinkingTo
Suggests	BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://github.com/ivanek/Gviz
BugReports	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_1.42.1.tar.gz
Windows Binary	Gviz_1.42.1.zip
macOS Binary (x86_64)	Gviz_1.42.1.tgz
macOS Binary (arm64)	Gviz_1.42.1.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 3.16	Source Archive