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DNAcopy specifications

Information


Unique identifier OMICS_00720
Name DNAcopy
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.34.0
Stability Stable
Maintained Yes

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  • person_outline Venkatraman E. Seshan <>

Publication for DNAcopy

DNAcopy in pipeline

2013
PMCID: 3813709
PMID: 24204606
DOI: 10.1371/journal.pone.0076251

[…] number 6.0 (biodiscovery, inc., ca, usa) was used to assess genome wide copy number frequencies for the 15 patients. further, aroma.affymetrix – another cbs implementation as part of bioconductor's dnacopy library and the associated tumorboost algorithm (which normalize allele specific copy numbers for tumor samples with paired normals) were also used to identify genomic events. we obtained […]


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DNAcopy in publications

 (64)
PMCID: 5789360
PMID: 29300322
DOI: 10.3390/cancers10010010

[…] package (partek inc., st. louis, mo, usa). in addition, we used gene network [] and david v6.8 [] to validate our findings by partek., pseudo probe data were generated with samtools varscan2 and dnacopy [,,]. briefly, when frozen tumor tissue was used for the isolation of high quality dna samples, pseudo-probe-derived gc-normalized log2 copy number ratios were generated for each sample using […]

PMCID: 5762307
PMID: 29340039
DOI: 10.18632/oncotarget.22560

[…] were sorted and removed with samtools 0.1.19 and picard tools 1.51 and local realignment and quality score recalibration was done with gatk version 2.1-13. copy number analysis was performed using dnacopy (v1.44.0) in r (v3.2.3) []. the parental v16d cell line was used as the comparator in the copy number analysis., we used rnaseq derived expression and gene-level copy number data as input […]

PMCID: 5595870
PMID: 28900112
DOI: 10.1038/s41467-017-00650-0

[…] window normalized by the cg content and dat represents the total sequenced data volume (gb). next, we integrated these windows into segments based on the circular binary segmentation algorithm from dnacopy package in r., to more accurately determine the allele-specific cn, we applied sequenza r package 2.1.1 to evaluate cn states among all whole-exome sequenced samples. standard bam files […]

PMCID: 5461742
PMID: 28592326
DOI: 10.1186/s13073-017-0442-0

[…] reads were trimmed using cutadapt []. genomic copy number data were produced by cnanorm [] after first aligning to the human reference genome (hg19) using bwa []. breakpoints were called using dnacopy []. human papilloma virus (hpv) infection was tested by re-aligning the data to known viral genomes []., tumour cell content was estimated using cnanorm, in conjunction with histological […]

PMCID: 5301398
PMID: 28183275
DOI: 10.1186/s12864-017-3531-y

[…] s5)., cnv calling was performed with 3 inherently different approaches to mitigate method specific errors: r-gada [] was used with the following parameters: alpha = 0.2, t = 4.5, minseglen = 5. dnacopy [] was used with minseglen = 5, undosd = 3, undoprune = 0.05 and data smoothing was applied prior to cnv calling. copymap [] was used with r = 20, t = 4, m = 5, a = 2.1, p = 0.001. […]


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DNAcopy institution(s)
Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA

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