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CopyNumberPlots

Create Copy-Number Plots using karyoploteR functionality

Bioconductor version: Release (3.17)

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 (from within R, enter citation("CopyNumberPlots")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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 PDF
NEWS Text

Details

biocViews CopyNumberVariation, Coverage, DNASeq, DataImport, OneChannel, Sequencing, Software, Visualization
Version 1.16.0
In Bioconductor since BioC 3.9 (R-3.6) (4.5 years)
License Artistic-2.0
Depends R (>= 3.6), karyoploteR
Imports regioneR, IRanges, Rsamtools, SummarizedExperiment, VariantAnnotation, methods, stats, GenomeInfoDb, GenomicRanges, cn.mops, rhdf5, utils
Linking To
Suggests BiocStyle, knitr, rmarkdown, panelcn.mops, BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat
System Requirements
Enhances
URL https://github.com/bernatgel/CopyNumberPlots
Bug Reports https://github.com/bernatgel/CopyNumberPlots/issues
See More
Depends On Me
Imports Me CNVfilteR, CNViz
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CopyNumberPlots_1.16.0.tar.gz
Windows Binary CopyNumberPlots_1.16.0.zip (64-bit only)
macOS Binary (x86_64) CopyNumberPlots_1.16.0.tgz
macOS Binary (arm64) CopyNumberPlots_1.16.0.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