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Bioconductor - Gviz (development version)

Gviz

This is the development version of Gviz; for the stable release version, see Gviz.

Plotting data and annotation information along genomic coordinates

Bioconductor version: Development (3.22)

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] ORCID: 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], Mike Smith [ctb]

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

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("Gviz")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Gviz")

Details biocViews Microarray, Sequencing, Software, Visualization Version 1.53.1 In Bioconductor since BioC 2.10 (R-2.15) (13.5 years) License Artistic-2.0 Depends R (>= 4.3), methods, S4Vectors(>= 0.9.25), IRanges(>= 1.99.18), GenomicRanges(>= 1.61.1), grid Imports XVector(>= 0.5.7), rtracklayer(>= 1.69.1), lattice, RColorBrewer, biomaRt(>= 2.11.0), AnnotationDbi(>= 1.27.5), Biobase(>= 2.15.3), GenomicFeatures(>= 1.61.4), ensembldb(>= 2.11.3), BSgenome(>= 1.77.1), Biostrings(>= 2.77.2), biovizBase(>= 1.13.8), Rsamtools(>= 2.25.1), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14), GenomicAlignments(>= 1.45.1), Seqinfo, GenomeInfoDb, BiocGenerics(>= 0.11.3), digest (>= 0.6.8), graphics, grDevices, stats, utils System Requirements URL https://github.com/ivanek/Gviz Bug Reports https://github.com/ivanek/Gviz/issues See More Suggests BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr, rmarkdown, testthat Linking To Enhances Depends On Me biomvRCNS, chimeraviz, cicero, cummeRbund, Pviz, methylationArrayAnalysis, rnaseqGene, csawBook Imports Me AllelicImbalance, ASpli, CAGEfightR, comapr, crisprViz, DMRcate, DuplexDiscovereR, ELMER, epimutacions, GenomicInteractions, maser, mCSEA, MEAL, methylPipe, motifbreakR, OGRE, primirTSS, regutools, RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.RiboMethSeq, SPLINTER, srnadiff, tadar, trackViewer, TVTB, uncoverappLib, VariantFiltering, DMRcatedata Suggests Me annmap, BindingSiteFinder, cellbaseR, CNVRanger, ensembldb, extraChIPs, fishpond, GenomicRanges, gwascat, interactiveDisplay, MIRit, pqsfinder, QuasR, RnBeads, segmenter, SplicingGraphs, TFutils, Single.mTEC.Transcriptomes, CAGEWorkflow, chipseqDB, chicane, GRIN2, RTIGER Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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