DOI: 10.18129/B9.bioc.Gviz    

This is the development version of Gviz; to use it, please install the devel version of Bioconductor.

Plotting data and annotation information along genomic coordinates

Bioconductor version: Development (3.10)

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]

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

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


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HTML R Script The Gviz User Guide
PDF   Reference Manual


biocViews Microarray, Sequencing, Software, Visualization
Version 1.29.0
In Bioconductor since BioC 2.10 (R-2.15) (7 years)
License Artistic-2.0
Depends R (>= 2.10.0), 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), 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)
Suggests BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, kableExtra, rmarkdown, testthat
URL https://github.com/ivanek/Gviz
BugReports https://github.com/ivanek/Gviz/issues
Depends On Me biomvRCNS, chimeraviz, cicero, coMET, cummeRbund, DMRforPairs, methylationArrayAnalysis, Pbase, Pviz, rnaseqGene
Imports Me AllelicImbalance, ASpli, CAGEfightR, DMRcate, ELMER, GeneStructureTools, GenomicInteractions, GGtools, InPAS, maser, mCSEA, MEAL, methyAnalysis, methylPipe, motifbreakR, Pi, PING, primirTSS, SPLINTER, STAN, trackViewer, TVTB, VariantFiltering
Suggests Me annmap, CAGEWorkflow, cellbaseR, chipseqDB, CNEr, csawUsersGuide, DeepBlueR, ensembldb, GenomicRanges, gwascat, interactiveDisplay, InterMineR, pqsfinder, QuasR, RnBeads, Single.mTEC.Transcriptomes, SplicingGraphs, TFutils, TxRegInfra
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Source Package Gviz_1.29.0.tar.gz
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Source Repository git clone https://git.bioconductor.org/packages/Gviz
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Package Short Url http://bioconductor.org/packages/Gviz/
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