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 (3.15)

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 <markus.riester at novartis.com>, Angad P. Singh <markus.riester at novartis.com>

Maintainer: Markus Riester <markus.riester at novartis.com>

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


To install this package, start R (version "4.2") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


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biocViews CopyNumberVariation, Coverage, ImmunoOncology, Sequencing, Software, VariantAnnotation, VariantDetection
Version 2.1.0
In Bioconductor since BioC 3.3 (R-3.3) (5.5 years)
License Artistic-2.0
Depends R (>= 3.5.0), 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, Biobase, Biostrings, BiocGenerics, rtracklayer, ggplot2, gridExtra, futile.logger, VGAM, tools, methods, mclust, rhdf5, Matrix
Suggests BiocParallel, BiocStyle, PSCBS, R.utils, TxDb.Hsapiens.UCSC.hg19.knownGene, copynumber, covr, knitr, optparse, org.Hs.eg.db, jsonlite, markdown, rmarkdown, testthat
Enhances genomicsdb (>= 0.0.3)
URL https://github.com/lima1/PureCN
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macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/PureCN
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PureCN
Package Short Url https://bioconductor.org/packages/PureCN/
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