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Copynumber specifications


Unique identifier OMICS_11158
Name Copynumber
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.20.0
Stability Stable
BiocGenerics, IRanges, GenomicRanges, S4Vectors, R(>=2.10)
Maintained Yes


No version available



  • person_outline Gro Nilsen

Publication for Copynumber

Copynumber citations


Evolution of Barrett’s esophagus through space and time at single crypt and whole biopsy levels

Nat Commun
PMCID: 5824808
PMID: 29476056
DOI: 10.1038/s41467-017-02621-x

[…] ypt sample was marginal for SNP array analysis, results were post-processed to remove areas of noisy signal shared across samples from different patients. Segments were jointly segmented based on the copynumber package and the ASCAT software was used for genotyping. The phangorn and BEAST packages were used for phylogenetic and evolutionary analyses. In order to estimate SCA mutation rates we deve […]


Single cell replication profiling to measure stochastic variation in mammalian replication timing

Nat Commun
PMCID: 5789892
PMID: 29382831
DOI: 10.1038/s41467-017-02800-w

[…] The corrected smoothed data was segmented using PCF (R copynumber package) to identify segments with similar copy number. The parameters used were γ = 3 and kmin = 5. Next, the segmented data at 50 kb resolution was used to binarize the domains as replica […]


A Carcinogen induced mouse model recapitulates the molecular alterations of human muscle invasive bladder cancer

PMCID: 5886988
PMID: 29367767
DOI: 10.1038/s41388-017-0099-6

[…] Cellularity, ploidy and intra-tumor variant allele frequencies were determined using Sequenza [] and an in-house modified version of copynumber [] that allowed segmentation of the mm10 genome. Adjusted intra-tumor variant allele frequencies were computed by dividing variant allele frequencies by the corresponding tumor cellularity. […]


CINdex: A Bioconductor Package for Analysis of Chromosome Instability in DNA Copy Number Data

Cancer Inform
PMCID: 5761903
PMID: 29343938
DOI: 10.1177/1176935117746637

[…] rofiles.Bioconductor is an open-source, open-development repository of software packages built using the R programming language. Bioconductor has several copy number segmentation algorithms including copynumber, fastseg, Vega, SMAP, and biomvRCNS. There are several copy number segmentation algorithms outside of Bioconductor, including Fused Margin Regression (FMR) and CBS.One of the challenges wit […]


DNA aneuploidy relationship with patient age and tobacco smoke in OPMDs/OSCCs

PLoS One
PMCID: 5587305
PMID: 28877236
DOI: 10.1371/journal.pone.0184425
call_split See protocol

[…] ged over replicates, and used as input for segmentation as follows: after probe value winsorization, data were segmented using the pcf or the multipcf function available in the R/BioConductor package copynumber with default settings []. Segments were considered aberrant if their log2 ratio values were above 0.32 for copy gains and below -0.41 for copy losses, based on the assumption of a minimum c […]


A Total variation Constrained Permutation Model for Revealing Common Copy Number Patterns

Sci Rep
PMCID: 5575355
PMID: 28851906
DOI: 10.1038/s41598-017-09139-8

[…] n (CBS), a statistical approach used in a single-cell sequencing protocol, is a modification of binary segmentation to translate a noisy intensity read depth signal into regions of equal copy number. Copynumber combines least squares principles with a suitable penalization scheme for a given number of breakpoints and detects copy number profiles. Control-FREEC (control-free copy number and allelic […]


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Copynumber institution(s)
Biomedical Informatics, Department of Informatics, University of Oslo, Oslo, Norway; Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway; Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK; Department of Human Genetics, VIB and University of Leuven, Leuven, Belgium; Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital Radiumhospitalet, Oslo, Norway; Department of Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; Breast Cancer Functional Genomics, Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge, Li Ka-Shing Centre, Cambridge, UK; Cambridge Breast Unit, Addenbrookes Hospital and Cambridge National Institute for Health Research Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK

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