CopywriteR

DOI: 10.18129/B9.bioc.CopywriteR  

Copy number information from targeted sequencing using off-target reads

Bioconductor version: Release (3.16)

CopywriteR extracts DNA copy number information from targeted sequencing by utiizing off-target reads. It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.

Author: Thomas Kuilman

Maintainer: Oscar Krijgsman <o.krijgsman at nki.nl>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("CopywriteR")

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("CopywriteR")

 

PDF	R Script	CopywriteR
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation, Coverage, ExomeSeq, ImmunoOncology, Preprocessing, Software, TargetedResequencing, Visualization
Version	2.29.0
In Bioconductor since	BioC 3.1 (R-3.2) (8 years)
License	GPL-2
Depends	R (>= 3.2), BiocParallel
Imports	matrixStats, gtools, data.table, S4Vectors, chipseq, IRanges, Rsamtools, DNAcopy, GenomicAlignments, GenomicRanges, CopyhelpeR, GenomeInfoDb, futile.logger
LinkingTo
Suggests	BiocStyle, SCLCBam, snow
SystemRequirements
Enhances
URL	https://github.com/PeeperLab/CopywriteR
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	CopywriteR_2.29.0.tar.gz
Windows Binary	CopywriteR_2.30.0.zip
macOS Binary (x86_64)	CopywriteR_2.30.0.tgz
macOS Binary (arm64)	CopywriteR_2.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CopywriteR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CopywriteR
Bioc Package Browser	https://code.bioconductor.org/browse/CopywriteR/
Package Short Url	https://bioconductor.org/packages/CopywriteR/
Package Downloads Report	Download Stats