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karyoploteR

Plot customizable linear genomes displaying arbitrary data

Bioconductor version: 3.23 · Package version: 1.38.0

karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

Installation

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

BiocManager::install("karyoploteR")

Details

MaintainerBernat Gel <bgel@igtp.cat>
AuthorBernat Gel [aut, cre] (ORCID: <https://orcid.org/0000-0001-8878-349X>)
LicenseArtistic-2.0
URLhttps://github.com/bernatgel/karyoploteR
Bug Reportshttps://github.com/bernatgel/karyoploteR/issues
Downloads rank1436
Source branchRELEASE_3_23
biocViewsChIPSeq, CopyNumberVariation, Coverage, DNASeq, DataImport, MethylSeq, OneChannel, Sequencing, Software, Visualization

Documentation

Download

Dependencies

Depends: R (>= 3.4), regioneR, GenomicRanges, methods

Imports: regioneR, GenomicRanges, IRanges, Rsamtools, stats, graphics, memoise, rtracklayer, Seqinfo, GenomeInfoDb, S4Vectors, biovizBase, digest, bezier, GenomicFeatures, bamsignals, AnnotationDbi, grDevices, VariantAnnotation

Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Hs.eg.db, org.Mm.eg.db, pasillaBamSubset

Reverse dependencies

Depends On Me (1): CopyNumberPlots

Imports Me (4): CNVfilteR, CNViz, fourSynergy, multicrispr

Suggests Me (5): Category, EpiMix, MitoHEAR, TmCalculator, UPDhmm