netClass protocols

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netClass specifications

Information


Unique identifier OMICS_02241
Name netClass
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
Stability Stable
Maintained Yes

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Publication for netClass

netClass in pipeline

2017
PMCID: 5737078
PMID: 28645144
DOI: 10.1093/nar/gkx554

[…] n50 value of less than 1 mb, we kept all nets that score >100 000 and kept all nested nets that align to the same locus (inversions or local translocations; net type ‘inv’ or ‘syn’ according to netclass) if they score >5000. for all other species, we kept all nets that score >10 000 and kept all nested nets of type ‘inv’ or ‘syn’ if they score >3000 (). note that these thresholds […]


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netClass in publications

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

[…] the quality measure of mo optimization process. the introduced algorithm integrates a weighted network from multiple omics data sets and optimizes the weighted networks., cun and frohlich, presented netclass algorithm of joining networks using smoothing approach. it uses smoothing method (kernel-based smoothing network diffusion) on the feature-wise marginal statistics over the structure […]

PMCID: 5374559
PMID: 28361683
DOI: 10.1186/s12859-017-1462-x

[…] 80 disease) [] and gse35713 (79 normal vs. 57 disease) []. the compared methods include gsva [], pathifier [], stsvm [], frsvm [] and aep []. as stsvm, frsvm and aep have been integrated into the netclass package [], we used the netclass package directly. due to gsva and pathifier implemented without feature selection, we select the same number biomarkers as identified by cns through svm-rfe […]

PMCID: 5295029
PMID: 28098823
DOI: 10.3390/genes8010035

[…] to select features by a permutation test with subsequent svm training. prediction performance was assessed by 10-time repeated 10-fold cross-validation. all calculations were performed through netclass r-package []., level 3 files of hnscc mirna and gene expression data present in the cancer genome atlas (tcga) [] were downloaded along with the clinical annotations from the tcga website [] […]

PMCID: 5059623
PMID: 27731320
DOI: 10.1038/srep34841

[…] function of limma r package. sam statistics were computed with the samr (http://cran.r-project.org/package=samr) r package, using parameters “two class unpaired” and “wilcoxon”. the netclass r package was used as implementaton of stsvm., how to cite this article: bersanelli, m. et al. network diffusion-based analysis of high-throughput data for the detection of differentially […]

PMCID: 4769543
PMID: 26921029
DOI: 10.1186/s12859-016-0951-7

[…] for encapp, there are two parameters α and λ in the elastic net model, where α is fixed as described below and λ is chosen by a 10-fold cross-validation. svm-aep is implemented with r package “netclass” using default parameters []., there are three parameters α,λ and r in the proposed model which require multi-parameter optimization based on cross-validation and grid search. however, […]


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netClass institution(s)
Bonn-Aachen International Center for IT (B-IT), University of Bonn, Bonn, Germany

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