Ulgen, E. | Search bioRxiv

bioRxiv2020

driveR: A Novel Method for Prioritizing Cancer Driver Genes Using Somatic Genomics Data

Cancer develops due to "driver" alterations. Numerous approaches exist for predicting cancer drivers from cohort-scale genomic data. However, methods for personalized analysis of driver genes are underdeveloped. In this study, we developed a novel personalized/batch analysis approach for driver gene prioritization utilizing somatic genomic data, called driveR. Combining genomic information and prior biological knowledge, driveR accurately prioritizes cancer driver genes via a multi-task learning model. Testing on 28 different datasets, this study demonstrates that driveR performs adequately, outperforms existing approaches, and is an accurate and easy-to-utilize approach for prioritizing driver genes in cancer genomes. driveR is available on CRAN: https://cran.r-project.org/package=driveR.

bioinformatics↗

bioRxiv2018

pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks

SummaryPathfindR is a tool for pathway enrichment analysis utilizing active subnetworks. It identifies gene sets that form active subnetworks in a protein-protein interaction network using a list of genes provided by the user. It then performs pathway enrichment analyses on the identified gene sets. Further, using the R package pathview, it maps the user data on the enriched pathways and renders pathway diagrams with the mapped genes. Because many of the enriched pathways are usually biologically related, pathfindR also offers functionality to cluster these pathways and identify representative pathways in the clusters. PathfindR is built as a stand-alone package but it can easily be integrated with other tools, such as differential expression/methylation analysis tools, for building fully automated pipelines. In this article, an overview of pathfindR is provided and an example application on a rheumatoid arthritis dataset is presented and discussed.\n\nAvailabilityThe package is freely available under MIT license at: https://github.com/egeulgen/pathfindR

bioinformatics↗