rScudo: Signature-based Clustering for Diagnostic Purposes

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 sample is computed using a method similar to GSEA. The graph of samples can the be used to perform community clustering or to perform supervised classification of samples in a testing set.

Installation

To install this package, install the devtools package and run:

devtools::install_github("Matteo-Ciciani/rScudo")

This package requires R >= 3.6.

Documentation

After installing the package, you can read the vignette for an overview of the package functionalities:

browseVignettes("rScudo")

Bug reports

Bugs should be reported at https://github.com/Matteo-Ciciani/rScudo/issues.