rScudo-package: Signature-based Clustering for Diagnostic Purposes

In Matteo-Ciciani/scudo: Signature-based Clustering for Diagnostic Purposes

Signature-based Clustering for Diagnostic Purposes

Description

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.

Author(s)

Matteo Ciciani [e-mail], Thomas Cantore [e-mail]

See Also

scudoTrain, scudoNetwork, scudoClassify

Examples

# To learn more about rScudo, start with the vignette:
browseVignettes("rScudo")

Matteo-Ciciani/scudo documentation built on Feb. 3, 2024, 9:41 a.m.