karyoploteR

DOI: 10.18129/B9.bioc.karyoploteR    

Plot customizable linear genomes displaying arbitrary data

Bioconductor version: Release (3.7)

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>

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

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

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

Details

biocViews ChIPSeq, CopyNumberVariation, Coverage, DNASeq, DataImport, MethylSeq, OneChannel, Sequencing, Software, Visualization
Version 1.6.1
In Bioconductor since BioC 3.5 (R-3.4) (1.5 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
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
Build Report  

Package Archives

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

Source Package karyoploteR_1.6.1.tar.gz
Windows Binary karyoploteR_1.6.1.zip
Mac OS X 10.11 (El Capitan) karyoploteR_1.6.1.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
Old Source Packages for BioC 3.7 Source Archive

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