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karyoploteR

Plot customizable linear genomes displaying arbitrary data


Bioconductor version: Release (3.19)

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.

Author: Bernat Gel [aut, cre]

Maintainer: Bernat Gel <bgel at igtp.cat>

Citation (from within R, enter citation("karyoploteR")):

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("karyoploteR")

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("karyoploteR")
karyoploteR vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, CopyNumberVariation, Coverage, DNASeq, DataImport, MethylSeq, OneChannel, Sequencing, Software, Visualization
Version 1.30.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License Artistic-2.0
Depends R (>= 3.4), regioneR, GenomicRanges, methods
Imports regioneR, GenomicRanges, IRanges, Rsamtools, stats, graphics, memoise, rtracklayer, GenomeInfoDb, S4Vectors, biovizBase, digest, bezier, GenomicFeatures, bamsignals, AnnotationDbi, grDevices, VariantAnnotation
System Requirements
URL https://github.com/bernatgel/karyoploteR
Bug Reports https://github.com/bernatgel/karyoploteR/issues
See More
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
Linking To
Enhances
Depends On Me CopyNumberPlots
Imports Me CNVfilteR, CNViz, multicrispr
Suggests Me Category, EpiMix, UPDhmm, MitoHEAR
Links To Me
Build Report Build Report

Package Archives

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

Source Package karyoploteR_1.30.0.tar.gz
Windows Binary karyoploteR_1.30.0.zip
macOS Binary (x86_64) karyoploteR_1.30.0.tgz
macOS Binary (arm64) karyoploteR_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/karyoploteR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/karyoploteR
Bioc Package Browser https://code.bioconductor.org/browse/karyoploteR/
Package Short Url https://bioconductor.org/packages/karyoploteR/
Package Downloads Report Download Stats