BridgeDbR

The software tool 'BridgeDbR' introduces PathVisioRPC, an XMLRPC interface for the pathway analysis software PathVisio. PathVisioRPC facilitates the creation, editing, and visualization of biological pathways, performing pathway statistics, and exporting results directly within scripting languages like R. It enables seamless integration of primary data analysis and pathway analysis, supporting tasks such as quality control, normalization, and statistical analysis. Additionally, it supports existing pathways from WikiPathways and automates repetitive visualization and analysis tasks.

Topic

Data identity and mapping;Rare diseases

Detail

  • Operation: Loading;ID mapping

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: The GNU General Public License v3.0

  • Cost: Free

  • Version name: 2.12.0

  • Credit: The Netherlands Consortium for Systems Biology (NCSB), part of the Netherlands Genomics Initiative/Netherlands Organisation for Scientific Research, the Google Summer of Code program 2012.

  • Input: Gene identifier [Textual format], Reaction ID [Textual format], Protein identifier [Textual format], Compound identifier [Textual format]

  • Output: Gene identifier [Textual format], Reaction ID [Textual format], Protein identifier [Textual format], Compound identifier [Textual format]

  • Contact: Egon Willighagen egon.willighagen@gmail.com

  • Collection: -

  • Maturity: Mature

Publications

  • Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment.
  • Bohler A, Eijssen LM, van Iersel MP, Leemans C, Willighagen EL, Kutmon M, Jaillard M, Evelo CT. Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment. BMC Bioinformatics. 2015 Aug 23;16(1):267. doi: 10.1186/s12859-015-0708-8. PMID: 26298294; PMCID: PMC4546821.
  • https://doi.org/10.1186/s12859-015-0708-8
  • PMID: 26298294
  • PMC: PMC4546821

Download and documentation

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