BioPAX-Parser: parsing and enrichment analysis of BioPAX pathways

SUMMARY Biological pathways are fundamental for learning about healthy and disease states. Many existing formats support automatic software analysis of biological pathways, for examples BioPAX (Biological Pathway Exchange). Although some algorithms are available as web application or standalone tools, no general graphical application for the parsing of BioPAX pathway data exists. Also, very few tools can perform Pathway Enrichment Analysis (PEA) using pathway encoded in the BioPAX format. To fill this gap we introduce BiP, an automatic and graphical software tool aimed at performing the parsing and accessing of BioPAX pathway data, along with pathway enrichment analysis by using information coming from pathways encoded in BioPAX. AVAILABILITY BiP is freely available for academic and non-profit organizations at https://gitlab.com/giuseppeagapito/bip under the LGPL 2.1, the GNU Lesser General Public License. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

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