TY - JOUR
T1 - gep2pep: a Bioconductor package for the creation and analysis of pathway-based expression profiles.
AU - Napolitano, Farancesco
AU - Carrella, Diego
AU - Gao, Xin
AU - di Bernardo, Diego
N1 - KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: Funding: This work has been supported by Fondazione Telethon and Fondazione Veronesi.
PY - 2019/10/25
Y1 - 2019/10/25
N2 - 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.
AB - 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.
UR - http://hdl.handle.net/10754/660056
UR - https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz803/5606711
U2 - 10.1093/bioinformatics/btz803
DO - 10.1093/bioinformatics/btz803
M3 - Article
C2 - 31647521
SN - 1367-4803
JO - Bioinformatics (Oxford, England)
JF - Bioinformatics (Oxford, England)
ER -