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

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

doi:10.1093/bioinformatics/btz803

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

Bioinformatics. 2019 Oct 24;36(6):1944-1945. doi: 10.1093/bioinformatics/btz803. Online ahead of print.

Authors

Farancesco Napolitano^{1

2}, Diego Carrella¹, Xin Gao², Diego di Bernardo¹

Affiliations

¹ Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, Pozzuoli (NA), Italy.
² Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.

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.