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CMDS specifications

Information


Unique identifier OMICS_02601
Name CMDS
Software type Application/Script
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Affymetrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Qunyuan Zhang

Publication for CMDS

CMDS citations

 (4)
library_books

CNV CH: A Convex Hull Based Segmentation Approach to Detect Copy Number Variations (CNV) Using Next Generation Sequencing Data

2015
PLoS One
PMCID: 4546278
PMID: 26291322
DOI: 10.1371/journal.pone.0135895

[…] cts CNVs at the nucleotide level. cnMOPS [] detects CNVs across multiple samples using a mixture of Poisson model. Another multiple sample analysis method is correlation matrix diagonal segmentation (CMDs) []. CMDs is based on a between-chromosomal site correlation analysis and is used to detect recurrent copy number aberrations (RCNA). As the input, it takes the copy numbers or CN data of genomic […]

library_books

Computational characterisation of cancer molecular profiles derived using next generation sequencing

2015
PMCID: 4322529
PMID: 25691827
DOI: 10.5114/wo.2014.47137

[…] posed to mutations, there is no accurate model established to identify genes with recurrent copy number aberrations (CNAs); therefore, methods are based on a non-parametric approach, e.g. GISTIC2 [], CMDS [], and ADMIRE [].(2) Prediction of the functional impact of individual mutations is based on the utilisation of additional information about protein sequence and/or structure and evolutionary co […]

library_books

Computational tools for copy number variation (CNV) detection using next generation sequencing data: features and perspectives

2013
BMC Bioinformatics
PMCID: 3846878
PMID: 24564169
DOI: 10.1186/1471-2105-14-S11-S1

[…] can be achieved by JointSLM with more samples [].JointSLM is not the only tool to utilize multiple samples to detect CNVs. Two additional tools, cn.MOPS and correlation matrix diagonal segmentation (CMDS), are proposed to increase statistical power and decrease computational burden based on a multiple samples approach. cn.MOPS proposed a data processing pipeline using a mixture of Poisson models […]

library_books

A Multi Sample Based Method for Identifying Common CNVs in Normal Human Genomic Structure Using High Resolution aCGH Data

2011
PLoS One
PMCID: 3205051
PMID: 22073121
DOI: 10.1371/journal.pone.0026975

[…] We also compared the MGVD results with those obtained using CMDS , which was recent recurrent CNV detection algorithm. Recurrent CNVs mean the common CNVs across multiple samples. Both MGVD and CMDS were designed to identify common CNVs; however, CMDS did not […]

Citations

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CMDS institution(s)
Division of Statistical Genomics, Washington University School of Medicine, St Louis, MO, USA; The Genome Center, Washington University School of Medicine, St Louis, MO, USA

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