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Package: Gviz
Title: Plotting data and annotation information along genomic coordinates
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Version: 1.40.1
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Authors@R: c(person("Florian", "Hahne", role="aut"),
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person("Steffen", "Durinck", role="aut"),
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person("Robert", "Ivanek", role=c("aut", "cre"),
email="robert.ivanek@unibas.ch",
comment=c(ORCID="0000-0002-8403-056X")),
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person("Arne", "Mueller", role="aut"),
person("Steve", "Lianoglou", role="aut"),
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person("Ge", "Tan", role="aut"),
person("Lance", "Parsons", role="aut"),
person("Shraddha", "Pai", role="aut"),
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person("Thomas", "McCarthy", role="ctb"),
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person("Felix", "Ernst", role="ctb"),
person("Mike", "Smith", role="ctb"))
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Description: Genomic data analyses requires integrated visualization
of known genomic information and new experimental data. Gviz uses
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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.
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LazyLoad: yes
Encoding: UTF-8
RoxygenNote: 7.1.2
Roxygen: list(markdown = TRUE)
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Depends:
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R (>= 4.2),
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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),
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ensembldb (>= 2.11.3),
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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),
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digest(>= 0.6.8),
graphics,
grDevices,
stats,
utils
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Suggests:
BSgenome.Hsapiens.UCSC.hg19,
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xml2,
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BiocStyle,
knitr,
rmarkdown,
testthat
biocViews: Visualization, Microarray, Sequencing
URL: https://github.com/ivanek/Gviz
BugReports: https://github.com/ivanek/Gviz/issues
VignetteBuilder: knitr
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License: Artistic-2.0
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Collate:
'utils.R'
'ImageMap-class.R'
'DisplayPars-class.R'
'GdObject-class.R'
'ReferenceTrack-class.R'
'SequenceTrack-class.R'
'RangeTrack-class.R'
'StackedTrack-class.R'
'NumericTrack-class.R'
'DataTrack-class.R'
'AlignmentsTrack-class.R'
'AnnotationTrack-class.R'
'GeneRegionTrack-class.R'
'BiomartGeneRegionTrack-class.R'
'CustomTrack-class.R'
'GenomeAxisTrack-class.R'
'Gviz-defunct.R'
'Gviz-deprecated.R'
'HighlightTrack-class.R'
'IdeogramTrack-class.R'
'OverlayTrack-class.R'
'UcscTrack.R'
'collapsing.R'
'datasets.R'
'exportTracks.R'
'grouping.R'
'plotTracks.R'
'settings.R'
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