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]|
|Bioconductor views||BiomedicalInformatics Classification Clustering DifferentialExpression FeatureExtraction GeneExpression GraphAndNetwork Network Proteomics SystemsBiology Transcriptomics|
|Maintainer||Matteo Ciciani <email@example.com>|
|Package repository||View on Bioconductor|
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