A Driver Discovery Tool for Cancer Whole Genomes
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"))
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.
BSgenome, BSgenome.Hsapiens.UCSC.hg19, Biostrings,
GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, plyr
Helen Zhu [aut, cre],
Juri Reimand [aut]

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")))
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>.
BSgenome, BSgenome.Hsapiens.UCSC.hg19, Biostrings,
GenomeInfoDb, GenomicRanges, IRanges, S4Vectors
knitr, testthat, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10,
rmarkdown
Juri Reimand [aut, cre],
Helen Zhu [aut]

BSgenome, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9,
BSgenome.Mmusculus.UCSC.mm10, Biostrings, GenomeInfoDb,
GenomicRanges, IRanges, S4Vectors

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")),
person("Kevin", "Cheng", email = "kevin.cheng@oicr.on.ca", role = "ctb"))
Juri Reimand [aut, cre],
Helen Zhu [aut],
Kevin Cheng [ctb]

c(person("Helen", "Zhu", email = "helen.zhu@oicr.on.ca", role = c("aut", "cre")),
person("Juri", "Reimand", email = "juri.reimand@utoronto.ca", role = "aut"),
person("Jonathan", "Barenboim", email = "jon.barenboim@gmail.com", role = "aut"))
An integrative method of analyzing multi omics data that conducts enrichment analysis of annotated gene sets. 'ActivePathways' uses a statistical data fusion approach, rationalizes contributing evidence and highlights associated genes, improving systems-level understanding of cellular organization in health and disease.
Helen Zhu [aut, cre],
Juri Reimand [aut],
Jonathan Barenboim [aut]