I would like to introduce our group's new R package for driver gene prioritization: driveR (latest release is v0.2).
driveR is a tool for personalized or batch analysis of genomics data for driver gene prioritization by combining genomics information and prior biological knowledge. As input, the tool requires ANNOVAR annotated CSV file (currently only hg19 is supported) and a data frame containing segment-level somatic copy-number alteration data.
As features, driveR uses coding impact metaprediction scores, non-coding impact scores, somatic copy number alteration scores, hotspot gene/double-hit gene condition, ‘phenolyzer’ gene scores and memberships to cancer-related KEGG pathways. It uses these features to estimate cancer-type-specific probabilities for each gene of being a cancer driver using the related task of a multi-task learning classification model.
You can read this vignette on how to run driveR for more detailed information.
You can install the released version of driveR from CRAN via:
And the development version from GitHub via:
install.packages("devtools") # if you have not installed this devtools::install_github("egeulgen/driveR")
You can read more about the method, its applications on 28 different datasets and comparison with other available methods in our 2020 preprint.
Find out more in the driveR website.