rScudo

DOI: 10.18129/B9.bioc.rScudo    

This is the development version of rScudo; for the stable release version, see rScudo.

Signature-based Clustering for Diagnostic Purposes

Bioconductor version: Development (3.17)

SCUDO (Signature-based Clustering for Diagnostic Purposes) is a rank-based method for the analysis of gene expression profiles for diagnostic and classification purposes. It is based on the identification of sample-specific gene signatures composed of the most up- and down-regulated genes for that sample. Starting from gene expression data, functions in this package identify sample-specific gene signatures and use them to build a graph of samples. In this graph samples are joined by edges if they have a similar expression profile, according to a pre-computed similarity matrix. The similarity between the expression profiles of two samples is computed using a method similar to GSEA. The graph of samples can then be used to perform community clustering or to perform supervised classification of samples in a testing set.

Author: Matteo Ciciani [aut, cre], Thomas Cantore [aut], Enrica Colasurdo [ctb], Mario Lauria [ctb]

Maintainer: Matteo Ciciani <matteo.ciciani at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("rScudo")

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("rScudo")

 

HTML	R Script	Signature-based Clustering for Diagnostic Purposes
PDF		Reference Manual

Details

biocViews	BiomedicalInformatics, Classification, Clustering, DifferentialExpression, FeatureExtraction, GeneExpression, GraphAndNetwork, Network, Proteomics, Software, SystemsBiology, Transcriptomics
Version	1.15.0
In Bioconductor since	BioC 3.9 (R-3.6) (3.5 years)
License	GPL-3
Depends	R (>= 3.6)
Imports	methods, stats, igraph, stringr, grDevices, Biobase, S4Vectors, SummarizedExperiment, BiocGenerics
LinkingTo
Suggests	testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel
SystemRequirements
Enhances
URL	https://github.com/Matteo-Ciciani/scudo
BugReports	https://github.com/Matteo-Ciciani/scudo/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	rScudo_1.15.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/rScudo
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rScudo
Package Short Url	https://bioconductor.org/packages/rScudo/
Package Downloads Report	Download Stats