<it>minet</it>: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information
<p>Abstract</p> <p>Results</p> <p>This paper presents the R/Bioconductor package <it>minet </it>(version 1.1.6) which provides a set of functions to infer mutual information networks from a dataset. Once fed with a microarray dataset, the package returns a n...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2008-10-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/9/461 |
| _version_ | 1818117734192381952 |
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| author | Bontempi Gianluca Lafitte Frédéric Meyer Patrick E |
| author_facet | Bontempi Gianluca Lafitte Frédéric Meyer Patrick E |
| author_sort | Bontempi Gianluca |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Results</p> <p>This paper presents the R/Bioconductor package <it>minet </it>(version 1.1.6) which provides a set of functions to infer mutual information networks from a dataset. Once fed with a microarray dataset, the package returns a network where nodes denote genes, edges model statistical dependencies between genes and the weight of an edge quantifies the statistical evidence of a specific (e.g transcriptional) gene-to-gene interaction. Four different entropy estimators are made available in the package <it>minet </it>(empirical, Miller-Madow, Schurmann-Grassberger and shrink) as well as four different inference methods, namely relevance networks, ARACNE, CLR and MRNET. Also, the package integrates accuracy assessment tools, like F-scores, PR-curves and ROC-curves in order to compare the inferred network with a reference one.</p> <p>Conclusion</p> <p>The package <it>minet </it>provides a series of tools for inferring transcriptional networks from microarray data. It is freely available from the Comprehensive R Archive Network (CRAN) as well as from the Bioconductor website.</p> |
| first_indexed | 2024-12-11T04:43:07Z |
| format | Article |
| id | doaj.art-5670ab9c39de40828bc07f42f7a667e0 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-11T04:43:07Z |
| publishDate | 2008-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-5670ab9c39de40828bc07f42f7a667e02022-12-22T01:20:34ZengBMCBMC Bioinformatics1471-21052008-10-019146110.1186/1471-2105-9-461<it>minet</it>: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual InformationBontempi GianlucaLafitte FrédéricMeyer Patrick E<p>Abstract</p> <p>Results</p> <p>This paper presents the R/Bioconductor package <it>minet </it>(version 1.1.6) which provides a set of functions to infer mutual information networks from a dataset. Once fed with a microarray dataset, the package returns a network where nodes denote genes, edges model statistical dependencies between genes and the weight of an edge quantifies the statistical evidence of a specific (e.g transcriptional) gene-to-gene interaction. Four different entropy estimators are made available in the package <it>minet </it>(empirical, Miller-Madow, Schurmann-Grassberger and shrink) as well as four different inference methods, namely relevance networks, ARACNE, CLR and MRNET. Also, the package integrates accuracy assessment tools, like F-scores, PR-curves and ROC-curves in order to compare the inferred network with a reference one.</p> <p>Conclusion</p> <p>The package <it>minet </it>provides a series of tools for inferring transcriptional networks from microarray data. It is freely available from the Comprehensive R Archive Network (CRAN) as well as from the Bioconductor website.</p>http://www.biomedcentral.com/1471-2105/9/461 |
| spellingShingle | Bontempi Gianluca Lafitte Frédéric Meyer Patrick E <it>minet</it>: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information BMC Bioinformatics |
| title | <it>minet</it>: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information |
| title_full | <it>minet</it>: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information |
| title_fullStr | <it>minet</it>: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information |
| title_full_unstemmed | <it>minet</it>: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information |
| title_short | <it>minet</it>: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information |
| title_sort | it minet it a r bioconductor package for inferring large transcriptional networks using mutual information |
| url | http://www.biomedcentral.com/1471-2105/9/461 |
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