CMDS statistics

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Associated diseases

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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

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Maintainer


  • person_outline Qunyuan Zhang <>

Publication for CMDS

CMDS in publications

 (4)
PMCID: 4322529
PMID: 25691827
DOI: 10.5114/wo.2014.47137

[…] 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 […]

PMCID: 3527554
PMID: 23285074
DOI: 10.1371/journal.pone.0052516

[…] null distribution, and its extension gistic2.0 considers the distinction of the background frequency between focal cnas and broad cnas and scores each marker proportional to its amplitude; cmds (correlation matrix diagonal segmentation) scores each marker based on its correlations with its surrounding sites and constructs a student’s t distribution; and dinamic (discovering copy […]

PMCID: 3432702
PMID: 22842228
DOI: 10.1038/ng.2359

[…] counts per gene. genes that had scna events in significantly more samples than expected were retained. we additionally required that these genes were located in chromosomal bands with significant cmds calls, as previously described,., we tested the melanoma risk snps rs1800401, rs1800407 (both in oca2), rs16891982 (slc45a2), rs1801516 (atm) and rs1126809 (tyr), all of which are located […]

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

[…] that this algorithm yielded. shows a comparison of the computational runtimes of mgvd and gada for real chromosomes of various sizes., 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 […]


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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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