karyoploteR

DOI: 10.18129/B9.bioc.karyoploteR    

Plot customizable linear genomes displaying arbitrary data

Bioconductor version: Release (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("karyoploteR")

Documentation

HTML	R Script	karyoploteR vignette
PDF		Reference Manual

Details

biocViews	ChIPSeq, CopyNumberVariation, Coverage, DNASeq, DataImport, MethylSeq, OneChannel, Sequencing, Software, Visualization
Version	1.4.2
In Bioconductor since	BioC 3.5 (R-3.4) (1 year)
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
LinkingTo
Suggests	BiocStyle, knitr, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	karyoploteR_1.4.2.tar.gz
Windows Binary	karyoploteR_1.4.2.zip
Mac OS X 10.11 (El Capitan)	karyoploteR_1.4.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/karyoploteR
Package Short Url	http://bioconductor.org/packages/karyoploteR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive