karyoploteR

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see karyoploteR.

Plot customizable linear genomes displaying arbitrary data

Bioconductor version: 3.21

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 iD ORCID: 0000-0001-8878-349X

Maintainer: Bernat Gel <bgel at igtp.cat>

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

Installation

To install this package, start R (version "4.5") 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 1.34.2

In Bioconductor since BioC 3.5 (R-3.4) (8.5 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

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_1.34.2.tar.gz

Windows Binary (x86_64) karyoploteR_1.34.2.zip

macOS Binary (x86_64) karyoploteR_1.34.2.tgz

macOS Binary (arm64) karyoploteR_1.34.2.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

Old Source Packages for BioC 3.21 Source Archive