CopywriteR

DOI: 10.18129/B9.bioc.CopywriteR  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.17 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CopywriteR.

Copy number information from targeted sequencing using off-target reads

Bioconductor version: Release (3.17)

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 "4.3") 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

PDF		Reference Manual

Details

biocViews	CopyNumberVariation, Coverage, ExomeSeq, ImmunoOncology, Preprocessing, Software, TargetedResequencing, Visualization
Version	2.32.0
In Bioconductor since	BioC 3.1 (R-3.2) (8.5 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
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/CopywriteR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CopywriteR
Package Short Url	https://bioconductor.org/packages/CopywriteR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive