RCy3: Network biology using Cytoscape from within R
| Autor: | Gustavsen, Julia A., Pai, Shraddha, Isserlin, Ruth, Demchak, Barry, Pico, Alexander R. |
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| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
Computer science
Interoperability Bioconductor computer.software_genre General Biochemistry Genetics and Molecular Biology 03 medical and health sciences Automation 0302 clinical medicine Use case General Pharmacology Toxicology and Pharmaceutics 030304 developmental biology 0303 health sciences General Immunology and Microbiology business.industry Software Tool Article Scripting Cytoscape General Medicine Articles Workflow Scripting language 030220 oncology & carcinogenesis Graph (abstract data type) Network biology Software engineering business computer 030217 neurology & neurosurgery Biological network |
| Zdroj: | F1000Research |
| ISSN: | 2046-1402 |
| Popis: | RCy3 is an R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort. Over 100 new functions have been added, including dozens of helper functions specifically for intuitive data overlay operations. Over 40 Cytoscape apps have implemented automation support so far, making hundreds of additional operations accessible via RCy3. Two-way conversion with networks from igraph and graph ensures interoperability with existing network biology workflows and dozens of other Bioconductor packages. These capabilities are demonstrated in a series of use cases involving public databases, enrichment analysis pipelines, shortest path algorithms and more. With RCy3, bioinformaticians will be able to quickly deliver reproducible network biology workflows as integrations of Cytoscape functions, complex custom analyses and other R packages. |
| Databáze: | OpenAIRE |
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