SVMDO
This is the development version of SVMDO; for the stable release version, see SVMDO.
Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by Disease Ontology
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Mustafa Erhan Ozer <erhanozer19 at marun.edu.tr>
citation("SVMDO")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text |
Details
| biocViews | Classification, DifferentialExpression, GUI, GeneSetEnrichment, RNASeq, Software, Survival, Transcriptomics |
| Version | 1.7.0 |
| 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 |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 3.1.6) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SVMDO_1.7.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |