karyoploteR
Plot customizable linear genomes displaying arbitrary data
Bioconductor version: 3.23 · Package version: 1.38.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("karyoploteR") Details
| Maintainer | Bernat Gel <bgel@igtp.cat> |
| Author | Bernat Gel [aut, cre] (ORCID: <https://orcid.org/0000-0001-8878-349X>) |
| License | Artistic-2.0 |
| URL | https://github.com/bernatgel/karyoploteR |
| Bug Reports | https://github.com/bernatgel/karyoploteR/issues |
| Downloads rank | 1436 |
| Source branch | RELEASE_3_23 |
| biocViews | ChIPSeq, CopyNumberVariation, Coverage, DNASeq, DataImport, MethylSeq, OneChannel, Sequencing, Software, Visualization |
Documentation
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Dependencies
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
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
Reverse dependencies
Depends On Me (1): CopyNumberPlots
Imports Me (4): CNVfilteR, CNViz, fourSynergy, multicrispr
Suggests Me (5): Category, EpiMix, MitoHEAR, TmCalculator, UPDhmm