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gep2pep: a Bioconductor package for the creation and analysis of pathway-based expression profiles.

dc.contributor.authorNapolitano, Farancesco
dc.contributor.authorCarrella, Diego
dc.contributor.authorGao, Xin
dc.contributor.authordi Bernardo, Diego
dc.date.accessioned2019-11-17T11:50:58Z
dc.date.available2019-11-17T11:50:58Z
dc.date.issued2019-10-25
dc.identifier.citationNapolitano, F., Carrella, D., Gao, X., & di Bernardo, D. (2019). gep2pep: a Bioconductor package for the creation and analysis of pathway-based expression profiles. Bioinformatics. doi:10.1093/bioinformatics/btz803
dc.identifier.doi10.1093/bioinformatics/btz803
dc.identifier.urihttp://hdl.handle.net/10754/660056
dc.description.abstractSUMMARY:Pathway-based expression profiles allow for high-level interpretation of transcriptomic data and systematic comparison of dysregulated cellular programs. We have previously demonstrated the efficacy of pathway-based approaches with two different applications: the Drug Set Enrichment Analysis and the Gene2drug analysis. Here we present a software tool that allows to easily convert gene-based profiles to pathway-based profiles and analyze them within the popular R framework. We also provide pre-computed profiles derived from the original Connectivity Map and its next generation release, i.e. the LINCS database. AVAILABILITY AND IMPLEMENTATION:the tool is implemented as the R/Bioconductor package gep2pep and can be freely downloaded from https://bioconductor.org/packages/gep2pep. SUPPLEMENTARY INFORMATION:Supplementary data are available at http://dsea.tigem.it/lincs.
dc.description.sponsorshipFunding: This work has been supported by Fondazione Telethon and Fondazione Veronesi.
dc.publisherOxford University Press (OUP)
dc.relation.urlhttps://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz803/5606711
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.titlegep2pep: a Bioconductor package for the creation and analysis of pathway-based expression profiles.
dc.typeArticle
dc.contributor.departmentComputational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.identifier.journalBioinformatics
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionTelethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, Pozzuoli (NA), Italy.
kaust.personNapolitano, Farancesco
kaust.personGao, Xin
refterms.dateFOA2019-11-17T11:52:30Z


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This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Except where otherwise noted, this item's license is described as This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.