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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

Versioning


No version available

Maintainer


  • person_outline Riku Louhimo

Publication for CNAmet

CNAmet citations

 (6)
library_books

Review of Statistical Learning Methods in Integrated Omics Studies (An Integrated Information Science)

2018
Bioinform Biol Insights
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 […]

library_books

DNA methylation signature (SAM40) identifies subgroups of the Luminal A breast cancer samples with distinct survival

2016
Oncotarget
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 […]

library_books

Integrative radiogenomic analysis for genomic signatures in glioblastomas presenting leptomeningeal dissemination

2016
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 […]

library_books

Public data and open source tools for multi assay genomic investigation of disease

2015
Brief Bioinform
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 […]

library_books

Systems medicine of inflammaging

2015
Brief Bioinform
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; […]

library_books

Relative impact of multi layered genomic data on gene expression phenotypes in serous ovarian tumors

2013
BMC Syst Biol
PMCID: 3906601
PMID: 24521303
DOI: 10.1186/1752-0509-7-S6-S9

[…] analysis approach with multi-dimensional genomics data, enabling the understanding of mechanisms that disturb regulatory/signalling cascades and downstream effects []. another relevant method, cnamet, is an r package for integrative analysis of high-throughput copy number, dna methylation, and gene expression data to identify genes that are amplified, hypomethylated and upregulated, […]


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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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