Registration Open for Bioc2024 July 24-26


Copy number calling and SNV classification using targeted short read sequencing

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

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


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


To view documentation for the version of this package installed in your system, start R and enter:

Best practices, quick start and command line usage HTML R Script
Overview of the PureCN R package PDF R Script
Reference Manual PDF


biocViews CopyNumberVariation, Coverage, ImmunoOncology, Sequencing, Software, VariantAnnotation, VariantDetection
Version 2.10.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
System Requirements
See More
Suggests BiocParallel, BiocStyle, PSCBS, R.utils, TxDb.Hsapiens.UCSC.hg19.knownGene, covr, knitr, optparse,, jsonlite, markdown, rmarkdown, testthat
Linking To
Enhances genomicsdb (>= 0.0.3)
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package PureCN_2.10.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) PureCN_2.10.0.tgz
macOS Binary (arm64) PureCN_2.10.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats