Gviz
Plotting data and annotation information along genomic coordinates
Bioconductor version: Release (3.19)
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] 
, 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("Gviz")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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")| The Gviz User Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Microarray, Sequencing, Software, Visualization |
| Version | 1.48.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (12.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.3), 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), ensembldb(>= 2.11.3), 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), 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 | Pviz, biomvRCNS, chimeraviz, cicero, cummeRbund, methylationArrayAnalysis, rnaseqGene, csawBook |
| Imports Me | ASpli, AllelicImbalance, CAGEfightR, DMRcate, ELMER, GenomicInteractions, MEAL, OGRE, PING, RNAmodR.AlkAnilineSeq, RNAmodR.RiboMethSeq, RNAmodR, SPLINTER, TVTB, VariantFiltering, comapr, crisprViz, epimutacions, mCSEA, maser, methylPipe, motifbreakR, primirTSS, regutools, srnadiff, tadar, trackViewer, uncoverappLib, DMRcatedata |
| Suggests Me | BindingSiteFinder, CNEr, CNVRanger, GenomicRanges, InterMineR, MIRit, QuasR, RnBeads, SplicingGraphs, TFutils, annmap, cellbaseR, ensembldb, extraChIPs, fishpond, gwascat, interactiveDisplay, pqsfinder, segmenter, Single.mTEC.Transcriptomes, CAGEWorkflow, chipseqDB, chicane, RTIGER |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Gviz_1.48.0.tar.gz |
| Windows Binary (x86_64) | Gviz_1.48.0.zip |
| macOS Binary (x86_64) | Gviz_1.48.0.tgz |
| macOS Binary (arm64) | Gviz_1.48.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Gviz |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Gviz |
| Bioc Package Browser | https://code.bioconductor.org/browse/Gviz/ |
| Package Short Url | https://bioconductor.org/packages/Gviz/ |
| Package Downloads Report | Download Stats |