karyoploteR

This is the released version of karyoploteR; for the devel version, see karyoploteR.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5

Plot customizable linear genomes displaying arbitrary data

Bioconductor version: Release (3.23)

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] ORCID: 0000-0001-8878-349X

Maintainer: Bernat Gel <bgel at igtp.cat>

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

Bernat Gel. karyoploteR: Plot customizable linear genomes displaying arbitrary data. doi:10.18129/B9.bioc.karyoploteR, R package version 1.38.0, https://bioconductor.org/packages/karyoploteR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ChIPSeq, CopyNumberVariation, Coverage, DNASeq, DataImport, MethylSeq, OneChannel, Sequencing, Software, Visualization
Version	1.38.0
In Bioconductor since	BioC 3.5 (R-3.4) (9.5 years)
License	Artistic-2.0
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
System Requirements
URL	https://github.com/bernatgel/karyoploteR
Bug Reports	https://github.com/bernatgel/karyoploteR/issues

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, fourSynergy, multicrispr
Suggests Me	Category, EpiMix, MitoHEAR, TmCalculator, UPDhmm
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	karyoploteR_1.38.0.tar.gz
Windows Binary (x86_64)	karyoploteR_1.38.0.zip
macOS Binary (big-sur-x86_64)	karyoploteR_1.38.0.tgz
macOS Binary (sonoma-arm64)	karyoploteR_1.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/karyoploteR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/karyoploteR
Package Short Url	https://bioconductor.org/packages/karyoploteR/
Package Downloads Report	Download Stats