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Gep2pep: a Bioconductor package for the creation and analysis of pathway-based expression profiles.

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.

SUBMITTER: Napolitano F

PROVIDER: S-EPMC7703749 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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

Napolitano Farancesco F Carrella Diego D Gao Xin X di Bernardo Diego D

Bioinformatics (Oxford, England) 20191024

<h4>Summary</h4>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 als ...[more]

PMID: 31647521

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