Package: SVMDO
Title: Identification of Tumor-Discriminating mRNA Signatures via
        Support Vector Machines Supported by Disease Ontology
Version: 1.11.0
Date: 2024-08-30
Authors@R: 
    c(person(given = "Mustafa Erhan",
	family = "Ozer",
    role = c("aut","cre"),
    comment = c(ORCID = "0000-0002-1572-8008"),
    email = "erhanozer19@marun.edu.tr"),
    person(given = "Pemra",
    family = "Ozbek Sarica",
    role = "aut",
    email = "pemra.ozbek@marmara.edu.tr"),
    person(given = "Kazim Yalcin",
    family = "Arga",
    role = "aut",
    email = "kazim.arga@marmara.edu.tr"))      
Depends: R(>= 4.4), shiny (>= 1.7.4)
Imports: shinyFiles (>= 0.9.3), shinytitle (>= 0.1.0), golem (>=
        0.3.5), nortest (>= 1.0-4), e1071 (>= 1.7-12), BSDA (>= 1.2.1),
        data.table (>= 1.14.6), sjmisc (>= 2.8.9), klaR (>= 1.7-1),
        caTools (>= 1.18.2), caret (>= 6.0-93), survival (>= 3.4-0), DT
        (>= 0.33.0), DOSE (>= 3.24.2), AnnotationDbi (>= 1.60.0),
        org.Hs.eg.db (>= 3.16.0), dplyr (>= 1.0.10),
        SummarizedExperiment (>= 1.28.0), grDevices, graphics, stats,
        utils
Description: It is an easy-to-use GUI using disease information for
        detecting tumor/normal sample discriminating gene sets from
        differentially expressed genes. Our approach is based on an
        iterative algorithm filtering genes with disease ontology
        enrichment analysis and wilk and wilks lambda criterion
        connected to SVM classification model construction. Along with
        gene set extraction, SVMDO also provides individual prognostic
        marker detection. The algorithm is designed for FPKM and RPKM
        normalized RNA-Seq transcriptome datasets.
RoxygenNote: 7.3.2
biocViews: GeneSetEnrichment, DifferentialExpression, GUI,
        Classification, RNASeq, Transcriptomics, Survival
NeedsCompilation: no
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.1.6)
VignetteBuilder: knitr
Config/testthat/edition: 3
BugReports: https://github.com/robogeno/SVMDO/issues
Config/pak/sysreqs: make libicu-dev libpng-dev libssl-dev libx11-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:23:08 UTC
RemoteUrl: https://github.com/bioc/SVMDO
RemoteRef: HEAD
RemoteSha: 2bc7e279332c5eae605d2fc16240613e753a7fd9
Packaged: 2025-10-30 13:41:16 UTC; root
Author: Mustafa Erhan Ozer [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1572-8008>),
  Pemra Ozbek Sarica [aut],
  Kazim Yalcin Arga [aut]
Maintainer: Mustafa Erhan Ozer <erhanozer19@marun.edu.tr>
Built: R 4.6.0; ; 2025-10-30 13:44:53 UTC; windows
