R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms
Putting new findings into the context of available literature knowledge is one approach to deal with the surge of high-throughput data results. Furthermore, prior knowledge can increase the performance and stability of bioinformatic algorithms, for example, methods for network reconstruction. In thi...
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| Format: | Article |
| Language: | English |
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MDPI AG
2014-02-01
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| Series: | Biology |
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| Online Access: | http://www.mdpi.com/2079-7737/3/1/85 |
| _version_ | 1797708138517889024 |
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| author | Frank Kramer Michaela Bayerlová Tim Beißbarth |
| author_facet | Frank Kramer Michaela Bayerlová Tim Beißbarth |
| author_sort | Frank Kramer |
| collection | DOAJ |
| description | Putting new findings into the context of available literature knowledge is one approach to deal with the surge of high-throughput data results. Furthermore, prior knowledge can increase the performance and stability of bioinformatic algorithms, for example, methods for network reconstruction. In this review, we examine software packages for the statistical computing framework R, which enable the integration of pathway data for further bioinformatic analyses. Different approaches to integrate and visualize pathway data are identified and packages are stratified concerning their features according to a number of different aspects: data import strategies, the extent of available data, dependencies on external tools, integration with further analysis steps and visualization options are considered. A total of 12 packages integrating pathway data are reviewed in this manuscript. These are supplemented by five R-specific packages for visualization and six connector packages, which provide access to external tools. |
| first_indexed | 2024-03-12T06:17:01Z |
| format | Article |
| id | doaj.art-a901622d66c44ed185d23bdaaa6f899a |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-12T06:17:01Z |
| publishDate | 2014-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-a901622d66c44ed185d23bdaaa6f899a2023-09-03T02:30:00ZengMDPI AGBiology2079-77372014-02-01318510010.3390/biology3010085biology3010085R-Based Software for the Integration of Pathway Data into Bioinformatic AlgorithmsFrank Kramer0Michaela Bayerlová1Tim Beißbarth2University Medical Center Göttingen, Department of Medical Statistics, Humboldtallee 32, D-37073 Göttingen, GermanyUniversity Medical Center Göttingen, Department of Medical Statistics, Humboldtallee 32, D-37073 Göttingen, GermanyUniversity Medical Center Göttingen, Department of Medical Statistics, Humboldtallee 32, D-37073 Göttingen, GermanyPutting new findings into the context of available literature knowledge is one approach to deal with the surge of high-throughput data results. Furthermore, prior knowledge can increase the performance and stability of bioinformatic algorithms, for example, methods for network reconstruction. In this review, we examine software packages for the statistical computing framework R, which enable the integration of pathway data for further bioinformatic analyses. Different approaches to integrate and visualize pathway data are identified and packages are stratified concerning their features according to a number of different aspects: data import strategies, the extent of available data, dependencies on external tools, integration with further analysis steps and visualization options are considered. A total of 12 packages integrating pathway data are reviewed in this manuscript. These are supplemented by five R-specific packages for visualization and six connector packages, which provide access to external tools.http://www.mdpi.com/2079-7737/3/1/85Pathway datadata integrationR-projectbioconductorBioPAXrBiopaxParserCytoscape |
| spellingShingle | Frank Kramer Michaela Bayerlová Tim Beißbarth R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms Biology Pathway data data integration R-project bioconductor BioPAX rBiopaxParser Cytoscape |
| title | R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms |
| title_full | R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms |
| title_fullStr | R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms |
| title_full_unstemmed | R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms |
| title_short | R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms |
| title_sort | r based software for the integration of pathway data into bioinformatic algorithms |
| topic | Pathway data data integration R-project bioconductor BioPAX rBiopaxParser Cytoscape |
| url | http://www.mdpi.com/2079-7737/3/1/85 |
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