CopyNumberPlots
This is the development version of CopyNumberPlots; for the stable release version, see CopyNumberPlots.
Create Copy-Number Plots using karyoploteR functionality
Bioconductor version: Development (3.24)
CopyNumberPlots have a set of functions extending karyoploteRs functionality to create beautiful, customizable and flexible plots of copy-number related data.
Author: Bernat Gel <bgel at igtp.cat> and Miriam Magallon <mmagallon at igtp.cat>
Maintainer: Bernat Gel <bgel at igtp.cat>
citation("CopyNumberPlots")):
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("CopyNumberPlots")
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("CopyNumberPlots")| CopyNumberPlots vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, Coverage, DNASeq, DataImport, OneChannel, Sequencing, Software, Visualization |
| Version | 1.29.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.6), karyoploteR |
| Imports | regioneR, IRanges, Rsamtools, SummarizedExperiment, VariantAnnotation, methods, stats, GenomeInfoDb, GenomicRanges, cn.mops, rhdf5, utils |
| System Requirements | |
| URL | https://github.com/bernatgel/CopyNumberPlots |
| Bug Reports | https://github.com/bernatgel/CopyNumberPlots/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, panelcn.mops, BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | CNVfilteR, CNViz |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CopyNumberPlots_1.29.0.tar.gz |
| Windows Binary (x86_64) | CopyNumberPlots_1.29.0.zip |
| macOS Binary (big-sur-x86_64) | CopyNumberPlots_1.29.0.tgz |
| macOS Binary (sonoma-arm64) | CopyNumberPlots_1.29.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CopyNumberPlots |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CopyNumberPlots |
| Bioc Package Browser | https://code.bioconductor.org/browse/CopyNumberPlots/ |
| Package Short Url | https://bioconductor.org/packages/CopyNumberPlots/ |
| Package Downloads Report | Download Stats |