Gviz
Plotting data and annotation information along genomic coordinates
Bioconductor version: 3.23 · Package version: 1.56.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Gviz") Details
| Maintainer | Robert Ivanek <robert.ivanek@unibas.ch> |
| Author | Florian Hahne [aut], Steffen Durinck [aut], Robert Ivanek [aut, cre] (ORCID: <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], Mike Smith [ctb] |
| License | Artistic-2.0 |
| URL | https://github.com/ivanek/Gviz |
| Bug Reports | https://github.com/ivanek/Gviz/issues |
| Downloads rank | 3861 |
| Source branch | RELEASE_3_23 |
| biocViews | Microarray, Sequencing, Software, Visualization |
Documentation
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Dependencies
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
Suggests: BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr, rmarkdown, testthat
Reverse dependencies
Depends On Me (7): biomvRCNS, chimeraviz, cicero, cummeRbund, methylationArrayAnalysis, Pviz, rnaseqGene
Imports Me (30): AllelicImbalance, ASpli, CAGEfightR, comapr, crisprViz, DMRcate, DMRcatedata, DuplexDiscovereR, ELMER, epimutacions, GeneStructureTools, GenomicInteractions, maser, mCSEA, MEAL, methylPipe, motifbreakR, OGRE, primirTSS, regutools, RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.RiboMethSeq, SPLINTER, srnadiff, tadar, trackViewer, TVTB, uncoverappLib, VariantFiltering
Suggests Me (22): annmap, BindingSiteFinder, CAGEWorkflow, cellbaseR, chicane, chipseqDB, CNEr, CNVRanger, ensembldb, extraChIPs, fishpond, GenomicRanges, GRIN2, gwascat, MIRit, pqsfinder, QuasR, RnBeads, segmenter, Single.mTEC.Transcriptomes, SplicingGraphs, TFutils