Package: SVMDO
Title: Identification of Tumor-Discriminating mRNA Signatures via
        Support Vector Machines Supported by Disease Ontology
Version: 1.2.8
Date: 2024-01-08
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(>= 4.3), 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 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: BiocStyle, knitr, rmarkdown, testthat (>= 3.1.6)
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_18
git_last_commit: e42b83d
git_last_commit_date: 2024-01-08
Repository: Bioconductor 3.18
Date/Publication: 2024-01-13
Packaged: 2024-01-14 07:58:53 UTC; biocbuild
Author: Mustafa Erhan Ozer [aut, cre] (<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 4.3.2; ; 2024-01-15 13:35:49 UTC; unix
