SCUDO

SCUDO is a tool for clustering gene expression profiles

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.

References

M Lauria. Rank-based transcriptional signatures: a novel approach to diagnostic biomarker definition and analysis, Systems Biomedicine 1 (4), 35-46, 2013. link

AL Tarca, M Lauria, M Unger, E Bilal, S Boue, KK Dey, J Hoeng, H Koeppl, et al. Strengths and limitations of microarray-based phenotype prediction: Lessons learned from the IMPROVER Diagnostic Signature Challenge, Bioinformatics 29 (22), 2892-2899, 2013. link

SCUDO: a tool for signature-based clustering of expression profiles Mario Lauria; Petros Moyseos; Corrado Priami Nucleic Acids Research 2015; link

rScudo: an R package for classification of molecular profiles using rank-based signatures link