karyoploteR
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see karyoploteR.
Plot customizable linear genomes displaying arbitrary data
Bioconductor version: 3.14
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("karyoploteR")):
Installation
To install this package, start R (version "4.1") 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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("karyoploteR")| karyoploteR vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, CopyNumberVariation, Coverage, DNASeq, DataImport, MethylSeq, OneChannel, Sequencing, Software, Visualization |
| Version | 1.20.3 |
| 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, GenomicFeatures, bamsignals, AnnotationDbi, grDevices, VariantAnnotation |
| System Requirements | |
| URL | https://github.com/bernatgel/karyoploteR |
| Bug Reports | https://github.com/bernatgel/karyoploteR/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, markdown, 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 |
| Linking To | |
| Enhances | |
| Depends On Me | CopyNumberPlots |
| Imports Me | CNVfilteR, CNViz, multicrispr, RIPAT |
| Suggests Me | Category |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | karyoploteR_1.20.3.tar.gz |
| Windows Binary | karyoploteR_1.20.3.zip |
| macOS 10.13 (High Sierra) | karyoploteR_1.20.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/karyoploteR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/karyoploteR |
| Bioc Package Browser | https://code.bioconductor.org/browse/karyoploteR/ |
| Package Short Url | https://bioconductor.org/packages/karyoploteR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.14 | Source Archive |