RCy3: Network biology using Cytoscape from within R.
Automation
Bioconductor
Cytoscape
Network biology
Scripting
Journal
F1000Research
ISSN: 2046-1402
Titre abrégé: F1000Res
Pays: England
ID NLM: 101594320
Informations de publication
Date de publication:
Historique:
accepted:
22
11
2019
entrez:
13
12
2019
pubmed:
13
12
2019
medline:
13
12
2019
Statut:
epublish
Résumé
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 \textit{igraph} and \textit{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.
Identifiants
pubmed: 31819800
doi: 10.12688/f1000research.20887.2
pmc: PMC6880260.2
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1774Informations de copyright
Copyright: © 2019 Gustavsen JA et al.
Déclaration de conflit d'intérêts
No competing interests were disclosed.