Package: SVMDO
Title: Identification of Tumor-Discriminating mRNA Signatures via
        Support Vector Machines Supported by Disease Ontology
Version: 1.0.0
Date: 2023-04-19
Authors@R: 
    c(person(given = "Mustafa Erhan",
	family = "Özer",
    role = c("aut","cre"),
    comment = c(ORCID = "0000-0002-1572-8008"),
    email = "erhanozer19@marun.edu.tr"),
    person(given = "Pemra",
    family = "Özbek Sarıca",
    role = "aut",
    email = "pemra.ozbek@marmara.edu.tr"),
    person(given = "Kazım Yalçın",
    family = "Arğa",
    role = "aut",
    email = "kazim.arga@marmara.edu.tr"))      
Depends: R(>= 4.3), 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),
        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’s 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.    
biocViews: GeneSetEnrichment, DifferentialExpression, GUI,
        Classification, RNASeq, Transcriptomics, Survival
NeedsCompilation: no
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Suggests: knitr, rmarkdown, testthat (>= 3.1.6), BiocStyle
VignetteBuilder: knitr
Config/testthat/edition: 3
BugReports: https://github.com/robogeno/SVMDO/issues
git_url: https://git.bioconductor.org/packages/SVMDO
git_branch: RELEASE_3_17
git_last_commit: 39afc67
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-25
Packaged: 2023-04-25 23:01:28 UTC; biocbuild
Author: Mustafa Erhan Özer [aut, cre] (<https://orcid.org/0000-0002-1572-8008>),
  Pemra Özbek Sarıca [aut],
  Kazım Yalçın Arğa [aut]
Maintainer: Mustafa Erhan Özer <erhanozer19@marun.edu.tr>
Built: R 4.3.1; ; 2023-07-20 07:32:59 UTC; unix
