Gviz

This is the development version of Gviz; for the stable release version, see Gviz.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10

Plotting data and annotation information along genomic coordinates

Bioconductor version: Development (3.24)

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] ORCID: 0000-0002-8403-056X , 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")):

Florian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Lianoglou, Ge Tan, Lance Parsons, Shraddha Pai. Gviz: Plotting data and annotation information along genomic coordinates. doi:10.18129/B9.bioc.Gviz, R package version 1.57.4, https://bioconductor.org/packages/Gviz.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Microarray, Sequencing, Software, Visualization
Version	1.57.4
In Bioconductor since	BioC 2.10 (R-2.15) (14.5 years)
License	Artistic-2.0
Depends	R (>= 4.3), methods, S4Vectors (>= 0.9.25), IRanges (>= 1.99.18), GenomicRanges (>= 1.61.1), grid
Imports	XVector (>= 0.5.7), rtracklayer (>= 1.69.1), lattice, RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5), Biobase (>= 2.15.3), GenomicFeatures (>= 1.61.4), ensembldb (>= 2.11.3), BSgenome (>= 1.77.1), Biostrings (>= 2.77.2), biovizBase (>= 1.13.8), Rsamtools (>= 2.25.1), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14), GenomicAlignments (>= 1.45.1), cigarillo, Seqinfo, GenomeInfoDb, 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

Suggests	BSgenome.Hsapiens.UCSC.hg38, xml2, BiocStyle, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me	biomvRCNS, chimeraviz, cicero, csawBook, methylationArrayAnalysis, Pviz, rnaseqGene
Imports Me	AllelicImbalance, ASpli, CAGEfightR, comapr, crisprViz, DMRcate, DMRcatedata, DuplexDiscovereR, ELMER, GeneStructureTools, GenomicInteractions, maser, mCSEA, MEAL, methylPipe, motifbreakR, OGRE, primirTSS, regutools, RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.RiboMethSeq, SPLINTER, srnadiff, tadar, TVTB, uncoverappLib, VariantFiltering
Suggests Me	annmap, BindingSiteFinder, CAGEWorkflow, cellbaseR, chicane, chipseqDB, CNEr, CNVRanger, ensembldb, epimutacions, extraChIPs, fishpond, GenomicRanges, GRIN2, gwascat, MIRit, pqsfinder, QuasR, RnBeads, segmenter, Single.mTEC.Transcriptomes, SplicingGraphs, TFutils, trackViewer, TSSr
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	Gviz_1.57.4.tar.gz
Windows Binary (x86_64)	Gviz_1.57.4.zip (64-bit only)
macOS Binary (big-sur-x86_64)	Gviz_1.57.4.tgz
macOS Binary (sonoma-arm64)	Gviz_1.57.4.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Gviz
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Gviz
Package Short Url	https://bioconductor.org/packages/Gviz/
Package Downloads Report	Download Stats