CopyNumberPlots

DOI: 10.18129/B9.bioc.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 (3.11)

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 "4.0") and enter:

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

# The following initializes usage of Bioc devel
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")

 

HTML R Script CopyNumberPlots vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews CopyNumberVariation, Coverage, DNASeq, DataImport, OneChannel, Sequencing, Software, Visualization
Version 1.3.1
In Bioconductor since BioC 3.9 (R-3.6) (0.5 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
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package CopyNumberPlots_1.3.1.tar.gz
Windows Binary CopyNumberPlots_1.3.1.zip
Mac OS X 10.11 (El Capitan) CopyNumberPlots_1.3.1.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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