Name Mode Size
accessors.R 100644 3 kb
class.R 100644 11 kb
packageDoc.R 100644 1 kb
scudoClassify.R 100644 10 kb
scudoClassifyUtilities.R 100644 5 kb
scudoCytoscape.R 100644 2 kb
scudoModel.R 100644 6 kb
scudoNetwork.R 100644 5 kb
scudoPlot.R 100644 2 kb
scudoTest.R 100644 6 kb
scudoTrain.R 100644 10 kb
show.R 100644 2 kb
utilities.R 100644 14 kb
## 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