rBiopaxParser—an R package to parse, modify and visualize BioPAX data
Motivation: Biological pathway data, stored in structured databases, is a useful source of knowledge for a wide range of bioinformatics algorithms and tools. The Biological Pathway Exchange (BioPAX) language has been established as a standard to store and annotate pathway information. However, use o...
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| Vydáno v: | Bioinformatics Ročník 29; číslo 4; s. 520 - 522 |
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| Hlavní autoři: | , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
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England
15.02.2013
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| ISSN: | 1367-4803, 1367-4811, 1367-4811, 1460-2059 |
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| Abstract | Motivation: Biological pathway data, stored in structured databases, is a useful source of knowledge for a wide range of bioinformatics algorithms and tools. The Biological Pathway Exchange (BioPAX) language has been established as a standard to store and annotate pathway information. However, use of these data within statistical analyses can be tedious. On the other hand, the statistical computing environment R has become the standard for bioinformatics analysis of large-scale genomics data. With this package, we hope to enable R users to work with BioPAX data and make use of the always increasing amount of biological pathway knowledge within data analysis methods.
Results: rBiopaxParser is a software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. These functions enable the user to access and modify specific parts of the BioPAX model. Furthermore, it allows to generate and layout regulatory graphs of controlling interactions and to visualize BioPAX pathways.
Availability: rBiopaxParser is an open-source R package and has been submitted to Bioconductor.
Contact: frank.kramer@med.uni-goettingen.de
Supplementary information: Supplementary data are available at Bioinformatics online. |
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| AbstractList | Biological pathway data, stored in structured databases, is a useful source of knowledge for a wide range of bioinformatics algorithms and tools. The Biological Pathway Exchange (BioPAX) language has been established as a standard to store and annotate pathway information. However, use of these data within statistical analyses can be tedious. On the other hand, the statistical computing environment R has become the standard for bioinformatics analysis of large-scale genomics data. With this package, we hope to enable R users to work with BioPAX data and make use of the always increasing amount of biological pathway knowledge within data analysis methods.MOTIVATIONBiological pathway data, stored in structured databases, is a useful source of knowledge for a wide range of bioinformatics algorithms and tools. The Biological Pathway Exchange (BioPAX) language has been established as a standard to store and annotate pathway information. However, use of these data within statistical analyses can be tedious. On the other hand, the statistical computing environment R has become the standard for bioinformatics analysis of large-scale genomics data. With this package, we hope to enable R users to work with BioPAX data and make use of the always increasing amount of biological pathway knowledge within data analysis methods.rBiopaxParser is a software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. These functions enable the user to access and modify specific parts of the BioPAX model. Furthermore, it allows to generate and layout regulatory graphs of controlling interactions and to visualize BioPAX pathways.RESULTSrBiopaxParser is a software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. These functions enable the user to access and modify specific parts of the BioPAX model. Furthermore, it allows to generate and layout regulatory graphs of controlling interactions and to visualize BioPAX pathways.rBiopaxParser is an open-source R package and has been submitted to Bioconductor.AVAILABILITYrBiopaxParser is an open-source R package and has been submitted to Bioconductor. Motivation: Biological pathway data, stored in structured databases, is a useful source of knowledge for a wide range of bioinformatics algorithms and tools. The Biological Pathway Exchange (BioPAX) language has been established as a standard to store and annotate pathway information. However, use of these data within statistical analyses can be tedious. On the other hand, the statistical computing environment R has become the standard for bioinformatics analysis of large-scale genomics data. With this package, we hope to enable R users to work with BioPAX data and make use of the always increasing amount of biological pathway knowledge within data analysis methods.Results: rBiopaxParser is a software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. These functions enable the user to access and modify specific parts of the BioPAX model. Furthermore, it allows to generate and layout regulatory graphs of controlling interactions and to visualize BioPAX pathways.Availability: rBiopaxParser is an open-source R package and has been submitted to Bioconductor.Contact: frank.kramer[at]med.uni-goettingen.deSupplementary information: Supplementary data are available at Bioinformatics online. Motivation: Biological pathway data, stored in structured databases, is a useful source of knowledge for a wide range of bioinformatics algorithms and tools. The Biological Pathway Exchange (BioPAX) language has been established as a standard to store and annotate pathway information. However, use of these data within statistical analyses can be tedious. On the other hand, the statistical computing environment R has become the standard for bioinformatics analysis of large-scale genomics data. With this package, we hope to enable R users to work with BioPAX data and make use of the always increasing amount of biological pathway knowledge within data analysis methods. Results: rBiopaxParser is a software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. These functions enable the user to access and modify specific parts of the BioPAX model. Furthermore, it allows to generate and layout regulatory graphs of controlling interactions and to visualize BioPAX pathways. Availability: rBiopaxParser is an open-source R package and has been submitted to Bioconductor. Contact: frank.kramer@med.uni-goettingen.de Supplementary information: Supplementary data are available at Bioinformatics online. Biological pathway data, stored in structured databases, is a useful source of knowledge for a wide range of bioinformatics algorithms and tools. The Biological Pathway Exchange (BioPAX) language has been established as a standard to store and annotate pathway information. However, use of these data within statistical analyses can be tedious. On the other hand, the statistical computing environment R has become the standard for bioinformatics analysis of large-scale genomics data. With this package, we hope to enable R users to work with BioPAX data and make use of the always increasing amount of biological pathway knowledge within data analysis methods. rBiopaxParser is a software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. These functions enable the user to access and modify specific parts of the BioPAX model. Furthermore, it allows to generate and layout regulatory graphs of controlling interactions and to visualize BioPAX pathways. rBiopaxParser is an open-source R package and has been submitted to Bioconductor. |
| Author | Kramer, Frank Bleckmann, Annalen Beißbarth, Tim Bayerlová, Michaela Klemm, Florian |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/23274212$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1093/bioinformatics/btm634 10.1089/152791601750294344 10.1093/bioinformatics/btq345 10.1093/bioinformatics/btr228 10.1093/nar/gkq1018 10.1016/S0076-6879(06)11018-6 10.1186/gb-2004-5-10-r80 10.1093/bioinformatics/bth458 10.1038/nbt.1666 10.1093/nar/gkn653 10.1093/nar/gkj126 10.1093/bioinformatics/btp167 10.1186/1471-2105-12-291 |
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| SubjectTerms | Algorithms Computational Biology Computer Graphics Databases, Factual Genomics Models, Biological Signal Transduction Software Vocabulary, Controlled |
| Title | rBiopaxParser—an R package to parse, modify and visualize BioPAX data |
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