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karyoploteR
This is thereleased version of karyoploteR; for the devel version, seekaryoploteR.
Plot customizable linear genomes displaying arbitrary data
Bioconductor version: Release (3.22)
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 [aut, cre]
ORCID: 0000-0001-8878-349X
Maintainer: Bernat Gel <bgel at igtp.cat>
citation("karyoploteR")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("karyoploteR")For older versions of R, please refer to the appropriateBioconductor 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 | 1.36.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (8.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.4),regioneR,GenomicRanges, methods |
| Imports | regioneR,GenomicRanges,IRanges,Rsamtools, stats, graphics,memoise,rtracklayer,Seqinfo,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 |
| Suggests Me | Category,EpiMix,UPDhmm,MitoHEAR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | karyoploteR_1.36.0.tar.gz |
| Windows Binary (x86_64) | karyoploteR_1.36.0.zip |
| macOS Binary (x86_64) | karyoploteR_1.36.0.tgz |
| macOS Binary (arm64) | karyoploteR_1.36.0.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 |