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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

Computational characterisation of cancer molecular profiles derived using next generation sequencing

2015
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 […]

library_books

Comparative Analysis of Methods for Identifying Recurrent Copy Number Alterations in Cancer

2012
PLoS One
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 […]

library_books

Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma

2012
Nat Genet
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 […]

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

[…] 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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