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DOI: 10.18129/B9.bioc.PureCN    

This is the development version of PureCN; for the stable release version, see PureCN.

Copy number calling and SNV classification using targeted short read sequencing

Bioconductor version: Development (3.7)

This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.

Author: Markus Riester [aut, cre], Angad P. Singh [aut]

Maintainer: Markus Riester <markus.riester at>

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PDF R Script PureCN overview
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PDF   Reference Manual
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biocViews CopyNumberVariation, Coverage, Sequencing, Software, VariantAnnotation, VariantDetection
Version 1.9.25
In Bioconductor since BioC 3.3 (R-3.3) (2 years)
License Artistic-2.0
Depends R (>= 3.3), DNAcopy, VariantAnnotation(>= 1.14.1)
Imports GenomicRanges(>= 1.20.3), IRanges(>= 2.2.1), RColorBrewer, S4Vectors, data.table, grDevices, graphics, stats, utils, SummarizedExperiment, GenomeInfoDb, GenomicFeatures, Rsamtools, Biostrings, BiocGenerics, rtracklayer, ggplot2, gridExtra, futile.logger, VGAM, tools, rhdf5, Matrix
Suggests PSCBS, BiocStyle, knitr, optparse, TxDb.Hsapiens.UCSC.hg19.knownGene,, testthat
Depends On Me
Imports Me
Suggests Me
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