Copynumber protocols

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 1.10.0
Stability Stable
Requirements BiocGenerics
Maintained Yes


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  • person_outline Gro Nilsen <>

Publication for Copynumber

Copynumber IN pipeline

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

[…] 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 package42 and the ascat43 software was used for genotyping. the phangorn44 and beast45 packages were used for phylogenetic and evolutionary analyses. in order to estimate sca mutation […]

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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