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PaxtoolsR: pathway analysis in R using Pathway Commons.

Augustin Luna1, Özgün Babur1, Bülent Arman Aksoy1

  • 1Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.

Bioinformatics (Oxford, England)
|December 20, 2015
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Summary
This summary is machine-generated.

The PaxtoolsR package provides R users with access to pathway data via Pathway Commons for advanced pathway analysis. It facilitates data extraction, merging, validation, and integration with local datasets.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Pathway analysis is crucial for understanding biological processes.
  • Accessing and integrating diverse pathway data can be challenging.
  • The R programming language is widely used in biological research.

Purpose of the Study:

  • To introduce PaxtoolsR, an R package for accessing and analyzing pathway data.
  • To enable advanced pathway analyses using data from Pathway Commons.
  • To facilitate the extraction, merging, validation, and integration of BioPAX data.

Main Methods:

  • Utilizes the Pathway Commons webservice for data retrieval.
  • Provides functions for querying, extracting, and merging pathway data.
  • Supports integration of online and local BioPAX datasets.

Main Results:

  • PaxtoolsR offers efficient access to comprehensive pathway datasets.
  • The package allows for robust data validation and merging capabilities.
  • Enables advanced querying and data integration for R users.

Conclusions:

  • PaxtoolsR enhances pathway analysis capabilities for R users.
  • The package simplifies the process of accessing and integrating biological pathway data.
  • It supports novel pathway datasets and advanced querying features.