karyoploteR

DOI: 10.18129/B9.bioc.karyoploteR    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see karyoploteR.

Plot customizable linear genomes displaying arbitrary data

Bioconductor version: 3.11

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 "4.0") 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 1.14.1
In Bioconductor since BioC 3.5 (R-3.4) (3.5 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
LinkingTo
Suggests BiocStyle, knitr, 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
SystemRequirements
Enhances
URL https://github.com/bernatgel/karyoploteR
BugReports https://github.com/bernatgel/karyoploteR/issues
Depends On Me CopyNumberPlots
Imports Me CNVfilteR
Suggests Me Category
Links To Me
Build Report  

Package Archives

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

Source Package karyoploteR_1.14.1.tar.gz
Windows Binary karyoploteR_1.14.1.zip
macOS 10.13 (High Sierra) karyoploteR_1.14.1.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 https://bioconductor.org/packages/karyoploteR/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: