karyoploteR
This is the development version of karyoploteR; for the stable release version, see karyoploteR.
Plot customizable linear genomes displaying arbitrary data
Bioconductor version: Development (3.24)
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.
Maintainer: Bernat Gel <bgel at igtp.cat>
citation("karyoploteR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.39.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 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, fourSynergy, multicrispr |
| Suggests Me | Category, EpiMix, UPDhmm, MitoHEAR, TmCalculator |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | karyoploteR_1.39.0.tar.gz |
| Windows Binary (x86_64) | karyoploteR_1.39.0.zip |
| macOS Binary (big-sur-x86_64) | karyoploteR_1.39.0.tgz |
| macOS Binary (sonoma-arm64) | karyoploteR_1.39.0.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 |