SVMDO

Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by Disease Ontology

Bioconductor version: Release (3.20)

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.

Author: Mustafa Erhan Ozer [aut, cre] , Pemra Ozbek Sarica [aut], Kazim Yalcin Arga [aut]

Maintainer: Mustafa Erhan Ozer <erhanozer19 at marun.edu.tr>

Citation (from within R, enter citation("SVMDO")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SVMDO")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SVMDO")

SVMDO-Tutorial	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, DifferentialExpression, GUI, GeneSetEnrichment, RNASeq, Software, Survival, Transcriptomics
Version	1.6.0
In Bioconductor since	BioC 3.17 (R-4.3) (1.5 years)
License	GPL-3
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
System Requirements
URL
Bug Reports	https://github.com/robogeno/SVMDO/issues

Suggests	BiocStyle, knitr, rmarkdown, testthat (>= 3.1.6)
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SVMDO_1.6.0.tar.gz
Windows Binary (x86_64)	SVMDO_1.6.0.zip
macOS Binary (x86_64)	SVMDO_1.6.0.tgz
macOS Binary (arm64)	SVMDO_1.5.5.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SVMDO
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SVMDO
Bioc Package Browser	https://code.bioconductor.org/browse/SVMDO/
Package Short Url	https://bioconductor.org/packages/SVMDO/
Package Downloads Report	Download Stats