driveR: driveR: An R Package for Prioritizing Cancer Driver Genes...

In driveR: Prioritizing Cancer Driver Genes Using Genomics Data

driveR: An R Package for Prioritizing Cancer Driver Genes Using Genomics Data

Description

Cancer genomes contain large numbers of somatic alterations but few genes drive tumor development. Identifying cancer driver genes is critical for precision oncology. Most of current approaches either identify driver genes based on mutational recurrence or using estimated scores predicting the functional consequences of mutations.

Details

driveR is a tool for personalized or batch analysis of genomic data for driver gene prioritization by combining genomic information and prior biological knowledge. 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.

Author(s)

Maintainer: Ege Ulgen [e-mail] (ORCID) [copyright holder]

See Also

predict_coding_impact for metaprediction of impact of coding variants. create_features_df for creating the features table to be used to prioritize cancer driver genes. See prioritize_driver_genes for prioritizing cancer driver genes

driveR documentation built on Aug. 19, 2023, 5:12 p.m.