Copynumber protocols

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Copynumber specifications

Information


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
Requirements
BiocGenerics, IRanges, GenomicRanges, S4Vectors, R(>=2.10)
Maintained Yes

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Documentation


Maintainer


  • person_outline Gro Nilsen <>

Publication for Copynumber

Copynumber in pipelines

 (3)
2018
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 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 […]

2018
PMCID: 5886988
PMID: 29367767
DOI: 10.1038/s41388-017-0099-6

[…] contains supplementary material, which is available to authorized users., the authors thank dr. francesco favero (technical university of denmark) for assistance with the use of the sequenza and copynumber r libraries, dr. vania vidimar (northwestern university) for insightful discussions and editorial assistance in writing the manuscript, and dr. andrea piunti (northwestern university) […]

2016
PMCID: 4726025
PMID: 26777065
DOI: 10.1038/srep19435

[…] probe location to the ncbi37/hg19 build of the human genome using the ucsc liftover utility (https://genome.ucsc.edu/cgi-bin/hgliftover), data were preprocessed by outlier winsorization with the copynumber package using default options, and segmented by penalized least square regression using a heuristically chosen value of γ = 100, which optimized the number of segments per sample, […]


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Copynumber in publications

 (18)
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 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 […]

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

[…] exclusivity was assessed by a fisher exact (one-tailed) test., 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 […]

PMCID: 5587305
PMID: 28877236
DOI: 10.1371/journal.pone.0184425

[…] 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 […]

PMCID: 5498998
PMID: 28683746
DOI: 10.1186/s12943-017-0691-y

[…] genotyping arrays with affymetrix power tools version 1.15.0 [, ] with hapmap samples as reference []. single-sample segmentation of normalized and gc corrected data was done with the r package copynumber (version 1.14.0) []. the user defined penalty parameter was set to 100. pcf value thresholds were set to ≥0.15 (gain) and ≤ −0.15 (loss). to enable comparison of samples with different […]

PMCID: 5491498
PMID: 28685159
DOI: 10.1038/s41523-017-0026-6

[…] as baseline control against which each tumour sample was normalised. the log2 ratios were smoothed by median absolute deviation and segmented by penalised least square regression using the library copynumber. estimates of cancer cell fraction and genomic mass were obtained using absolute and non-rounded estimates of copy numbers and copy number calls were obtained as described above for snp […]


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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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