CopyNumberPlots

DOI: 10.18129/B9.bioc.CopyNumberPlots    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see CopyNumberPlots.

Create Copy-Number Plots using karyoploteR functionality

Bioconductor version: 3.13

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 "4.1") and enter:

if (!requireNamespace("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")

 

HTML R Script CopyNumberPlots vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews CopyNumberVariation, Coverage, DNASeq, DataImport, OneChannel, Sequencing, Software, Visualization
Version 1.8.0
In Bioconductor since BioC 3.9 (R-3.6) (2.5 years)
License Artistic-2.0
Depends R (>= 3.6), karyoploteR
Imports regioneR, IRanges, Rsamtools, SummarizedExperiment, VariantAnnotation, methods, stats, GenomeInfoDb, GenomicRanges, cn.mops, rhdf5, utils
LinkingTo
Suggests BiocStyle, knitr, panelcn.mops, BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat
SystemRequirements
Enhances
URL https://github.com/bernatgel/CopyNumberPlots
BugReports https://github.com/bernatgel/CopyNumberPlots/issues
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_1.8.0.tar.gz
Windows Binary CopyNumberPlots_1.8.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) CopyNumberPlots_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CopyNumberPlots
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CopyNumberPlots
Package Short Url https://bioconductor.org/packages/CopyNumberPlots/
Package Downloads Report Download Stats

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