JBiclustGE: Java API with unified biclustering algorithms for gene expression data analysis
Over the last years, comparative studies of biclustering algorithms have been described in the literature, showing that a variety of programming languages were used in their development. Because of this fact, many researchers have difficulty using some of these methods, since it is necessary to setu...
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| Published in | Knowledge-based systems Vol. 155; pp. 83 - 87 |
|---|---|
| Main Authors | , |
| Format | Journal Article |
| Language | English |
| Published |
Amsterdam
Elsevier B.V
01.09.2018
Elsevier Elsevier Science Ltd |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0950-7051 1872-7409 |
| DOI | 10.1016/j.knosys.2018.04.024 |
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| Abstract | Over the last years, comparative studies of biclustering algorithms have been described in the literature, showing that a variety of programming languages were used in their development. Because of this fact, many researchers have difficulty using some of these methods, since it is necessary to setup an environment for running a given algorithm or to have some programming skills in order to compile it. We present a new Java API for biclustering analysis in the context of gene expression data, allowing the use of 21 biclustering algorithms, in a single application. It is freely available at https://jbiclustge.github.io as an open source framework. |
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| AbstractList | Over the last years, comparative studies of biclustering algorithms have been described in the literature, showing that a variety of programming languages were used in their development. Because of this fact, many researchers have difficulty using some of these methods, since it is necessary to setup an environment for running a given algorithm or to have some programming skills in order to compile it. We present a new Java API for biclustering analysis in the context of gene expression data, allowing the use of 21 biclustering algorithms, in a single application. It is freely available at https://jbiclustge.github.io as an open source framework. Over the last years, comparative studies of biclustering algorithms have been described in the literature, showing that a variety of programming languages were used in their development. Because of this fact, many researchers have difficulty using some of these methods, since it is necessary to setup an environment for running a given algorithm or to have some programming skills in order to compile it. We present a new Java API for biclustering analysis in the context of gene expression data, allowing the use of 21 biclustering algorithms, in a single application. It is freely available at https://jbiclustge.github.io as an open source framework. This work was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of DID/810/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). |
| Author | Rocha, Orlando Mendes, Rui |
| Author_xml | – sequence: 1 givenname: Orlando surname: Rocha fullname: Rocha, Orlando email: orocha@deb.uminho.pt organization: Center of Biological Engineering, University of Minho, Portugal – sequence: 2 givenname: Rui surname: Mendes fullname: Mendes, Rui email: rcm@di.uminho.pt organization: Department of Informatics, University of Minho, Portugal |
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| Cites_doi | 10.1093/bioinformatics/btn250 10.1093/bib/bbs032 10.1109/RBME.2010.2083647 10.1016/j.jbi.2015.06.028 10.1186/1742-4682-8-39 10.1093/bioinformatics/btn076 10.1371/journal.pone.0090801 10.1109/TCBB.2004.2 10.1016/j.cmpb.2009.12.003 10.1080/01621459.1972.10481214 10.1093/bioinformatics/btl099 10.1109/TKDE.2004.68 10.1093/bioinformatics/bti641 |
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| SubjectTerms | Algorithms Application programming interface Biclustering Comparative analysis Comparative studies Data analysis Data mining Gene expression Java Open source software Programming languages Science & Technology |
| Title | JBiclustGE: Java API with unified biclustering algorithms for gene expression data analysis |
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