karyoploteR

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see karyoploteR.

Plot customizable linear genomes displaying arbitrary data


Bioconductor version: 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>

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

Installation

To install this package, start R (version "3.4") 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

Reference Manual PDF

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) (7 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
System Requirements
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Suggests BiocStyle, knitr, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset
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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
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/karyoploteR
Package Short Url https://bioconductor.org/packages/karyoploteR/
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Old Source Packages for BioC 3.6 Source Archive