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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.

Functions (27)

AlignedReadTrack-class

DEPRECATED! AlignedReadTrack class and methods)

AlignmentsTrack-class

AlignmentsTrack class and methods

AnnotationTrack-class

AnnotationTrack class and methods

BiomartGeneRegionTrack-class

BiomartGeneRegionTrack class and methods

CustomTrack-class

CustomTrack class and methods

DataTrack-class

DataTrack class and methods

DisplayPars-class

DisplayPars class and method

GdObject-class

GdObject class and methods

GeneRegionTrack-class

GeneRegionTrack class and methods

GenomeAxisTrack-class

GenomeAxisTrack class and methods

Gviz-deprecated

Deprecated functions in package ‘Gviz’

HighlightTrack-class

HighlightTrack class and methods

IdeogramTrack-class

IdeogramTrack class and methods

ImageMap-class

ImageMap class and methods

NumericTrack-class

NumericTrack class and methods

OverlayTrack-class

OverlayTrack class and methods

RangeTrack-class

RangeTrack class and methods

ReferenceTrack-class

ReferenceTrack class and methods

SequenceTrack-class

SequenceTrack class and methods

StackedTrack-class

StackedTrack class and methods

UcscTrack

Meta-constructor for GenomeGraph tracks fetched directly from the various UCSC data sources.

collapsing

Dynamic content based on the available resolution

datasets

Data sets

exportTracks

Export GenomeGraph tracks to a annotation file representation.

grouping

Grouping of annotation features

plotTracks

The main plotting function for one or several GenomeGraph tracks.

settings

Setting display parameters to control the look and feel of the plots

Gviz

Plotting data and annotation information along genomic coordinates

v1.34.1

Artistic-2.0

Authors

Florian Hahne [aut], Steffen Durinck [aut], Robert Ivanek [aut, cre] (<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]

Initial release

Gviz

Functions (27)

Gviz

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