rScudo

DOI: 10.18129/B9.bioc.rScudo    

This is the development version of rScudo; to use it, please install the devel version of Bioconductor.

Signature-based Clustering for Diagnostic Purposes

Bioconductor version: Development (3.9)

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>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("rScudo", version = "3.9")

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")

 

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

Details

biocViews BiomedicalInformatics, Classification, Clustering, DifferentialExpression, FeatureExtraction, GeneExpression, GraphAndNetwork, Network, Proteomics, Software, SystemsBiology, Transcriptomics
Version 0.99.6
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_0.99.6.tar.gz
Windows Binary rScudo_0.99.6.zip
Mac OS X 10.11 (El Capitan) rScudo_0.99.6.tgz
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 http://bioconductor.org/packages/rScudo/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: