Package: driveR
Title: Prioritizing Cancer Driver Genes Using Genomics Data
Version: 0.1.1
Authors@R: 
    person(given = "Ege",
           family = "Ulgen",
           role = c("aut", "cre", "cph"),
           email = "egeulgen@gmail.com",
           comment = c(ORCID = "0000-0003-2090-3621"))
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Description: Cancer genomes contain large numbers of somatic alterations but few
    genes drive tumor development. Identifying molecular 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. '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 
    probability for each gene of being a cancer driver using the related task of 
    a multi-task learning classification model. The method is described in detail 
    in Ulgen E, Sezerman U. 2020. driveR: A Novel Method for Prioritizing Cancer 
    Driver Genes Using Somatic Genomics Data. bioRxiv 
    <doi:10.1101/2020.11.10.376707>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
URL: https://egeulgen.github.io/driveR/,
        https://github.com/egeulgen/driveR/
BugReports: https://github.com/egeulgen/driveR/issues
biocViews:
Imports: caret, randomForest, Homo.sapiens, GenomicRanges,
        GenomeInfoDb, GenomicFeatures,
        TxDb.Hsapiens.UCSC.hg19.knownGene, S4Vectors, org.Hs.eg.db,
        rlang
Depends: R (>= 4.0)
Suggests: testthat, covr, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-11-12 14:02:39 UTC; egeulgen
Author: Ege Ulgen [aut, cre, cph] (<https://orcid.org/0000-0003-2090-3621>)
Repository: CRAN
Date/Publication: 2020-11-18 10:10:08 UTC
