CopyNumberPlots

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see CopyNumberPlots.

Create Copy-Number Plots using karyoploteR functionality

Bioconductor version: 3.19

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 "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CopyNumberVariation, Coverage, DNASeq, DataImport, OneChannel, Sequencing, Software, Visualization

Version 1.20.0

In Bioconductor since BioC 3.9 (R-3.6) (5.5 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

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

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Package Archives

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

Source Package CopyNumberPlots_1.20.0.tar.gz

Windows Binary (x86_64) CopyNumberPlots_1.20.0.zip

macOS Binary (x86_64) CopyNumberPlots_1.20.0.tgz

macOS Binary (arm64) CopyNumberPlots_1.20.0.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/

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