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- Title
PaxtoolsR: pathway analysis in R using Pathway Commons.
- Authors
Luna, Augustin; Babur, Özgün; Aksoy, Bülent Arman; Demir, Emek; Sander, Chris
- Abstract
Purpose: PaxtoolsR package enables access to pathway data represented in the BioPAX format and made available through the Pathway Commons webservice for users of the R language to aid in advanced pathway analyses. Features include the extraction, merging and validation of pathway data represented in the BioPAX format. This package also provides novel pathway datasets and advanced querying features for R users through the Pathway Commons webservice allowing users to query, extract and retrieve data and integrate these data with local BioPAX datasets. Availability and implementation: The PaxtoolsR package is compatible with versions of R 3.1.1 (and higher) on Windows, Mac OS X and Linux using Bioconductor 3.0 and is available through the Bioconductor R package repository along with source code and a tutorial vignette describing common tasks, such as data visualization and gene set enrichment analysis. Source code and documentation are at http://www.bioconductor.org/packages/paxtoolsr. This plugin is free, open-source and licensed under the LGPL-3.
- Subjects
COMPUTER network resources; COMPUTER software; DATA distribution; BIOCONDUCTOR (Computer software); SOURCE code; OPEN source intelligence
- Publication
Bioinformatics, 2016, Vol 32, Issue 8, p1262
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btv733