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DOI: 10.18129/B9.bioc.Gviz    

Plotting data and annotation information along genomic coordinates

Bioconductor version: Release (3.5)

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, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Lianoglou, Ge Tan <ge.tan09 at>, Lance Parsons <lparsons at>, Shraddha Pai <shraddha.pai at>

Maintainer: Florian Hahne <florian.hahne at>

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PDF R Script Gviz users guide
PDF   Reference Manual
Text   NEWS


biocViews Microarray, Software, Visualization
Version 1.20.0
In Bioconductor since BioC 2.10 (R-2.15) (5.5 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 xtable, BSgenome.Hsapiens.UCSC.hg19, BiocStyle
Depends On Me biomvRCNS, chimeraviz, coMET, cummeRbund, DMRforPairs, Pbase, Pviz
Imports Me AllelicImbalance, ASpli, DMRcate, GenomicInteractions, GGtools, gwascat, InPAS, methyAnalysis, methylPipe, motifbreakR, Pi, PING, SPLINTER, STAN, trackViewer, TVTB, VariantFiltering
Suggests Me annmap, cellbaseR, CNEr, DeepBlueR, ensembldb, GenomicRanges, interactiveDisplay, pqsfinder, QuasR, RnBeads, Single.mTEC.Transcriptomes, SplicingGraphs
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