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

Farancesco Napolitano, Diego Carrella, Xin Gao, Diego di Bernardo

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

SUMMARY: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.
Original languageEnglish (US)
JournalBioinformatics (Oxford, England)
DOIs
StatePublished - Oct 25 2019

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