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: 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>

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


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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
Suggests BiocStyle, SCLCBam, snow
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