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CopywriteR

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

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>

Citation (from within R, enter citation("CopywriteR")):

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

Reference Manual PDF

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
Linking To
Suggests BiocStyle, SCLCBam, snow
System Requirements
Enhances
URL https://github.com/PeeperLab/CopywriteR
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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/
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