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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("karyoploteR")
In most cases, you don't need to download the package archive at all.
karyoploteR
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Plot customizable linear genomes displaying arbitrary data
Bioconductor version: Release (3.5)
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
| HTML | R Script | karyoploteR vignette |
| Reference Manual |
Details
| biocViews | ChIPSeq, CopyNumberVariation, Coverage, DNASeq, DataImport, MethylSeq, Sequencing, Software, Visualization |
| Version | 1.2.2 |
| In Bioconductor since | BioC 3.5 (R-3.4) (0.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.4), regioneR, GenomicRanges, methods |
| Imports | regioneR, GenomicRanges, 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_1.2.2.tar.gz |
| Windows Binary | karyoploteR_1.2.2.zip |
| Mac OS X 10.11 (El Capitan) | karyoploteR_1.2.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/karyoploteR |
| Package Short Url | http://bioconductor.org/packages/karyoploteR/ |
| Package Downloads Report | Download Stats |
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