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CopyNumberPlots

Create Copy-Number Plots using karyoploteR functionality


Bioconductor version: Release (3.18)

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 1.18.0
In Bioconductor since BioC 3.9 (R-3.6) (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_1.18.0.tar.gz
Windows Binary CopyNumberPlots_1.18.0.zip
macOS Binary (x86_64) CopyNumberPlots_1.18.0.tgz
macOS Binary (arm64) CopyNumberPlots_1.18.0.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