karyoploteR

DOI: 10.18129/B9.bioc.karyoploteR    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see karyoploteR.

Plot customizable linear genomes displaying arbitrary data

Bioconductor version: 3.8

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 <bgel at igtp.cat>

Maintainer: Bernat Gel <bgel at igtp.cat>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

HTML	R Script	karyoploteR vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, CopyNumberVariation, Coverage, DNASeq, DataImport, MethylSeq, OneChannel, Sequencing, Software, Visualization
Version	1.8.8
In Bioconductor since	BioC 3.5 (R-3.4) (2 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
LinkingTo
Suggests	BiocStyle, knitr, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, pasillaBamSubset
SystemRequirements
Enhances
URL	https://github.com/bernatgel/karyoploteR
BugReports	https://github.com/bernatgel/karyoploteR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	karyoploteR_1.8.8.tar.gz
Windows Binary	karyoploteR_1.8.8.zip
Mac OS X 10.11 (El Capitan)	karyoploteR_1.8.8.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	http://bioconductor.org/packages/karyoploteR/
Package Downloads Report	Download Stats