c("aut")), person("Lora", "Wu", , "L.Wu@massey.ac.nz", c("aut", "cre")),

Description: A mutation analysis tool that discovers cancer driver genes with frequent mutations in protein signalling sites such as post-translational modifications (phosphorylation, ubiquitination, etc). The Poisson generalised linear regression model identifies genes where cancer mutations in signalling sites are more frequent than expected from the sequence of the entire gene. Integration of mutations with signalling information helps find new driver genes and propose candidate mechanisms to known drivers. Reference: Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. Juri Reimand and Gary D Bader. Molecular Systems Biology (2013) 9:637 <doi:10.1038/msb.2012.68>.
Title: Finding Cancer Driver Proteins with Enriched Mutations in
Authors@R: person("Juri", "Reimand", email = "juri.reimand@utoronto.ca", role = c("aut", "cre"))
Packaged: 2017-08-23 18:26:21 UTC; dthompson

Title: A Driver Discovery Tool for Cancer Whole Genomes
Authors@R: c(person("Helen", "Zhu", email = "helen.zhu@oicr.on.ca", role = c("aut", "cre")),
person("Juri", "Reimand", email = "juri.reimand@oicr.on.ca", role = "aut"))
Description: A method for finding an enrichment of cancer simple somatic mutations (SNVs and Indels) in functional elements across the human genome. 'ActiveDriverWGS' detects coding and noncoding driver elements using whole genome sequencing data.
GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, plyr

Authors@R: c(person("Juri", "Reimand", email = "juri.reimand@utoronto.ca", role = c("aut", "cre")), person("Helen", "Zhu", email = "helen.zhu@oicr.on.ca", role = c("aut")))
Description: A method for finding an enrichment of cancer simple somatic mutations (SNVs and Indels) in functional elements across the human genome. 'ActiveDriverWGS' detects coding and noncoding driver elements using whole genome sequencing data. The method is part of the following publication: Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks. Molecular Cell (2020) <doi:10.1016/j.molcel.2019.12.027>.