NetSAM pipeline

NetSAM specifications

Information


Unique identifier OMICS_17527
Name NetSAM
Alternative name Network Seriation And Modularization
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data An edge-list representation of a network.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.16.0
Stability Stable
Requirements igraph, seriation, graph
Maintained Yes

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Documentation


Maintainer


  • person_outline Bing Zhang <>

NetSAM IN pipelines

 (4)
2013
PMCID: 3774028
PMID: 24073403
DOI: 10.1155/2013/401649

[…] parameters are set as default numbers. the significantly enriched functional modules based on kegg [8] pathway are investigated., in brief, go and pathway analyses indicate the effectiveness of the netsam, which highlights potential application of the method that may be prominent when developing targeted therapeutics. it is also reasonable to believe that the genes detected by the netsam […]

2013
PMCID: 3774028
PMID: 24073403
DOI: 10.1155/2013/401649

[…] of the netsam, which highlights potential application of the method that may be prominent when developing targeted therapeutics. it is also reasonable to believe that the genes detected by the netsam are highly relevant to cancer either by sharing common cancer-related signaling pathways or by go functional terms., in this section, results of experiments with synthetic and real-world data […]

2013
PMCID: 3774028
PMID: 24073403
DOI: 10.1155/2013/401649

[…] for medium-scale data, t-test and lasso typically cannot fully capture the relational complexity for large-scale datasets. experiments demonstrated the reliability and the effectiveness of the netsam algorithm. furthermore, our algorithm occupied a higher position in the accuracy/efficiency trade-off. in addition, validation of the biological reasonability of detected genes as biomarkers […]

2013
PMCID: 3774028
PMID: 24073403
DOI: 10.1155/2013/401649

[…] of the biological reasonability of detected genes as biomarkers was done through analysis of functional enrichment and a vast amount of independent literature., in order to estimate the accuracy of netsam algorithm and compare its performance with two commonly used gene-based algorithms, that is, t-test and lasso, we generated synthetic data sets by using the syntren [28], which simulates […]

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