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Copy number information from targeted sequencing using off-target reads

Bioconductor version: 3.1

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: Thomas Kuilman <t.kuilman at>

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PDF R Script CopywriteR
PDF   Reference Manual
Text   NEWS


biocViews CopyNumberVariation, Coverage, ExomeSeq, Preprocessing, Software, TargetedResequencing, Visualization
Version 2.0.6
In Bioconductor since BioC 3.1 (R-3.2) (< 6 months)
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
Depends On Me
Imports Me
Suggests Me
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