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CNAmet specifications

Information


Unique identifier OMICS_08998
Name CNAmet
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
Version 1.2.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Riku Louhimo <>

Publication for CNAmet

CNAmet in publications

 (6)
PMCID: 5824897
PMID: 29497285
DOI: 10.1177/1177932218759292

[…] minimization of ssc maximization uses m eigenvectors derived from the multiple data sets (studies) to form an eigenvector matrix., the publicly available software packages for meta-analysis include cnamet, rtopper, iclusterplus, and the stategra bioconductor package., we sought to give an overview of the existing methods in integrated omics presented in the past decade. the following discussion […]

PMCID: 5352035
PMID: 27911866
DOI: 10.18632/oncotarget.13718

[…] norway450k study cohort. samples correspond to those presented in figure ., to investigate whether the genes in the sam40 signature were affected concomitantly by methylation and genomic alteration cnamet analysis was performed on samples of the luminal a subtype. cnamet is an algorithm to analyze the simultaneous and synergistic (additive) effect of methylation and copy-number alteration […]

PMCID: 5058842
PMID: 27399113
DOI: 10.1097/MD.0000000000004109

[…] vector that was labeled 1 for amplification (log value >0) and 0 for no amplification. to identify the significant genes that exhibited cna and gene expression changes, we modified an r package (cnamet) that integrates high-throughput copy number data and expression data.[] cnamet algorithm followed next step. first, the signal-to-noise ratio statistic was used to link gene expression values […]

PMCID: 4945830
PMID: 26463000
DOI: 10.1093/bib/bbv080

[…] the aim is to refine findings based on one data type with additional analysis of further omics data obtained from the same set of samples. some of the available software in this category are cnamet [], rtopper [], iclusterplus [] and the stategra bioconductor package. we note that these methods fall short of full systems biology data integration, as they do not, for example, incorporate […]

PMCID: 4870395
PMID: 26307062
DOI: 10.1093/bib/bbv062

[…] altogether []. some multilayer integrative approaches, like icluster [] and mdi (multiple dataset integration) [], can be applied to several types of data sets, while others, such as camelot [] and cnamet [], were developed for specific combinations of omics. the integration strategies can be sequential or simultaneous: sequential approaches refine the results of one layer using further layers; […]


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CNAmet institution(s)
Computational Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Research Program, University of Helsinki, Finland
CNAmet funding source(s)
Academy of Finland (project 125826); Sigrid Jusélius Foundation, Finnish Cancer Associations and Biocentrum Helsinki

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