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.