Gviz: Plotting data and annotation information along genomic coordinates

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.

AuthorFlorian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller, Steve Lianoglou, Ge Tan <ge.tan09@imperial.ac.uk>, Lance Parsons <lparsons@princeton.edu>, Shraddha Pai <shraddha.pai@utoronto.ca>
Date of publicationNone
MaintainerFlorian Hahne <florian.hahne@novartis.com>
LicenseArtistic-2.0
Version1.18.1

View on Bioconductor

Files in this package

Gviz/DESCRIPTION
Gviz/NAMESPACE
Gviz/NEWS
Gviz/R
Gviz/R/AllClasses.R Gviz/R/AllGenerics.R Gviz/R/Gviz-methods.R Gviz/R/Gviz.R
Gviz/Rplots.pdf
Gviz/TODO
Gviz/build
Gviz/build/vignette.rds
Gviz/data
Gviz/data/alTrackGenes.rda
Gviz/data/biomTrack.rda
Gviz/data/bmTrack.rda
Gviz/data/collapseTrack.rda
Gviz/data/cpgIslands.rda
Gviz/data/cyp2b10.rda
Gviz/data/denseAnnTrack.rda
Gviz/data/dtHoriz.rda
Gviz/data/geneDetails.rda
Gviz/data/geneModels.rda
Gviz/data/idTrack.rda
Gviz/data/itrack.rda
Gviz/data/twoGroups.rda
Gviz/data/ucscItems.rda
Gviz/inst
Gviz/inst/CITATION
Gviz/inst/doc
Gviz/inst/doc/Gviz.R
Gviz/inst/doc/Gviz.Rnw
Gviz/inst/doc/Gviz.pdf
Gviz/inst/extdata
Gviz/inst/extdata/GSM461176_S2_DRSC_Untreated_1_bmm.bam
Gviz/inst/extdata/GSM461176_S2_DRSC_Untreated_1_bmm.bam.bai
Gviz/inst/extdata/GSM461179_S2_DRSC_CG8144_RNAi_1_bmm.bam
Gviz/inst/extdata/GSM461179_S2_DRSC_CG8144_RNAi_1_bmm.bam.bai
Gviz/inst/extdata/biomartVersionsLatest.txt
Gviz/inst/extdata/biomartVersionsNow.txt
Gviz/inst/extdata/gapped.bam
Gviz/inst/extdata/gapped.bam.bai
Gviz/inst/extdata/snps.bam
Gviz/inst/extdata/snps.bam.bai
Gviz/inst/extdata/test.2bit
Gviz/inst/extdata/test.bam
Gviz/inst/extdata/test.bam.bai
Gviz/inst/extdata/test.bed
Gviz/inst/extdata/test.bedGraph
Gviz/inst/extdata/test.bw
Gviz/inst/extdata/test.fa
Gviz/inst/extdata/test.fa.fai
Gviz/inst/extdata/test.gff
Gviz/inst/extdata/test.gff1
Gviz/inst/extdata/test.gff2
Gviz/inst/extdata/test.gff3
Gviz/inst/extdata/test.gtf
Gviz/inst/extdata/test.wig
Gviz/inst/lib
Gviz/inst/lib/testUCSC.pl
Gviz/inst/lib/ucscUrl.pl
Gviz/inst/scripts
Gviz/inst/scripts/documentation.R
Gviz/inst/scripts/functionality.R
Gviz/inst/scripts/loadIntoEnv.R
Gviz/inst/scripts/sourcePackage.R
Gviz/inst/scripts/testBiomartGenomeMappings.R
Gviz/inst/scripts/testing.R
Gviz/inst/scripts/updateBiomartGenomeMappings.R
Gviz/man
Gviz/man/AlignedReadTrack-class.Rd Gviz/man/AlignmentsTrack-class.Rd Gviz/man/AnnotationTrack-class.Rd Gviz/man/BiomartGeneRegionTrack-class.Rd Gviz/man/CustomTrack-class.Rd Gviz/man/DataTrack-class.Rd Gviz/man/DisplayPars-class.Rd Gviz/man/GdObject-class.Rd Gviz/man/GeneRegionTrack-class.Rd Gviz/man/GenomeAxisTrack-class.Rd Gviz/man/HighlightTrack-class.Rd Gviz/man/IdeogramTrack-class.Rd Gviz/man/ImageMap-class.Rd Gviz/man/NumericTrack-class.Rd Gviz/man/OverlayTrack-class.Rd Gviz/man/RangeTrack-class.Rd Gviz/man/ReferenceTrack-class.Rd Gviz/man/SequenceTrack-class.Rd Gviz/man/StackedTrack-class.Rd Gviz/man/UcscTrack.Rd Gviz/man/collapsing.Rd Gviz/man/datasets.Rd Gviz/man/exportTracks.Rd Gviz/man/grouping.Rd Gviz/man/plotTracks.Rd Gviz/man/settings.Rd
Gviz/vignettes
Gviz/vignettes/Gviz-refs.bib
Gviz/vignettes/Gviz.Rnw
Gviz/vignettes/ucsc1.pdf
Gviz/vignettes/ucsc2.pdf

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