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Gviz

Plotting data and annotation information along genomic coordinates

Bioconductor version: 3.23 · Package version: 1.56.0

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.

Installation

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

BiocManager::install("Gviz")

Details

MaintainerRobert Ivanek <robert.ivanek@unibas.ch>
AuthorFlorian Hahne [aut], Steffen Durinck [aut], Robert Ivanek [aut, cre] (ORCID: <https://orcid.org/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]
LicenseArtistic-2.0
URLhttps://github.com/ivanek/Gviz
Bug Reportshttps://github.com/ivanek/Gviz/issues
Downloads rank3861
Source branchRELEASE_3_23
biocViewsMicroarray, Sequencing, Software, Visualization

Documentation

Download

Dependencies

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), Seqinfo, GenomeInfoDb, BiocGenerics (>= 0.11.3), digest (>= 0.6.8), graphics, grDevices, stats, utils

Suggests: BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr, rmarkdown, testthat

Reverse dependencies

Depends On Me (7): biomvRCNS, chimeraviz, cicero, cummeRbund, methylationArrayAnalysis, Pviz, rnaseqGene

Imports Me (30): AllelicImbalance, ASpli, CAGEfightR, comapr, crisprViz, DMRcate, DMRcatedata, DuplexDiscovereR, ELMER, epimutacions, GeneStructureTools, GenomicInteractions, maser, mCSEA, MEAL, methylPipe, motifbreakR, OGRE, primirTSS, regutools, RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.RiboMethSeq, SPLINTER, srnadiff, tadar, trackViewer, TVTB, uncoverappLib, VariantFiltering

Suggests Me (22): annmap, BindingSiteFinder, CAGEWorkflow, cellbaseR, chicane, chipseqDB, CNEr, CNVRanger, ensembldb, extraChIPs, fishpond, GenomicRanges, GRIN2, gwascat, MIRit, pqsfinder, QuasR, RnBeads, segmenter, Single.mTEC.Transcriptomes, SplicingGraphs, TFutils