Package: driveR
Title: Prioritizing Cancer Driver Genes Using Genomics Data
Version: 0.5.0.9000
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
        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 OU. 2021. driveR: driveR: a novel
        method for prioritizing cancer driver genes using somatic
        genomics data. BMC Bioinformatics
        <doi:10.1186/s12859-021-04203-7>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
URL: https://egeulgen.github.io/driveR/,
        https://github.com/egeulgen/driveR
BugReports: https://github.com/egeulgen/driveR/issues
biocViews:
Imports: caret, randomForest, GenomicRanges, GenomeInfoDb,
        GenomicFeatures, S4Vectors, rlang,
Depends: R (>= 4.0)
Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Hsapiens.UCSC.hg38.knownGene, testthat, covr, knitr,
        rmarkdown
VignetteBuilder: knitr
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://egeulgen.r-universe.dev
Date/Publication: 2025-12-22 11:39:41 UTC
RemoteUrl: https://github.com/egeulgen/driver
RemoteRef: HEAD
RemoteSha: 1737978ecf7744ee558aa7cea0146df2e34461cb
NeedsCompilation: no
Packaged: 2026-06-23 07:46:40 UTC; root
Author: Ege Ulgen [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0003-2090-3621>)