AbsCN-seq specifications

Information


Unique identifier OMICS_02202
Name AbsCN-seq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Karen Messer <>

Publication for AbsCN-seq

AbsCN-seq in publications

 (3)
PMCID: 4682901
PMID: 26669540
DOI: 10.1371/journal.pone.0143811

[…] 41 patients, two showed poor quality in exome sequencing data, and the final exome analysis was done in 39 patients. absolute copy numbers based on copy-number variations of samples are inferred by abscn-seq [], and clonality analysis is performed by sciclone []. somatic mutations are calculated by varscan v2.3.6 and variants are annotated by in-house annotation pipeline., quantitative real […]

PMCID: 4640562
PMID: 26554380
DOI: 10.1371/journal.pone.0142487

[…] with agilent sureselect at targeted coverage depth of 50x for germline and 200-400x for tumor dna from fresh frozen specimens. tumor purity, ploidy and absolute copy numbers were estimated using abscn-seq []. we validated a selected set of called mutations from each tumor pair using targeted sequencing to depth 8000x (miseq; omegabiotek, inc.). for validation data, variants were called using […]

PMCID: 4563570
PMID: 26350498
DOI: 10.1038/srep13955

[…] variants but not original sequence reads. the formulation does not explicitly consider effects of copy number gains/losses and may bias tumor purity estimation. moreover, puriryest, theta, and abscn-seq rely on next-generation sequencing data, thus may not be applicable to existing copy number data acquired using more classic methods such as snp arrays., since bacom2.0 is supported […]


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AbsCN-seq institution(s)
Division of Biostatistics, Moores Cancer Center, University of California-San Diego, La Jolla, CA, USA

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