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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


No version available

Maintainer


  • person_outline Karen Messer

Publication for AbsCN-seq

AbsCN-seq citations

 (3)
library_books

The Clinical Significance and Molecular Features of the Spatial Tumor Shapes in Breast Cancers

2015
PLoS One
PMCID: 4682901
PMID: 26669540
DOI: 10.1371/journal.pone.0143811

[…] e 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. […]

library_books

Mutational Profiling Can Establish Clonal or Independent Origin in Synchronous Bilateral Breast and Other Tumors

2015
PLoS One
PMCID: 4640562
PMID: 26554380
DOI: 10.1371/journal.pone.0142487

[…] n to both tumors (, upper panel). There was an additional deletion in the distal end of 6q (6q25.1-6q27) apparent only in the TN tumor (, lower panel), covering the entire ESR1 locus. We then applied absCN-seq to estimate the absolute copy numbers for the ESR1 region () and found that the HR+ tumor has two copies and the TN tumor only one copy for this region. Thus a plausible evolutionary sequenc […]

library_books

BACOM2.0 facilitates absolute normalization and quantification of somatic copy number alterations in heterogeneous tumor

2015
Sci Rep
PMCID: 4563570
PMID: 26350498
DOI: 10.1038/srep13955

[…] eotide 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 by a well- […]

Citations

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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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