Package: rScudo 1.21.0
Matteo Ciciani
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 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.
Authors:
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rScudo.pdf |rScudo.html✨
rScudo/json (API)
NEWS
| # Install 'rScudo' in R: |
| install.packages('rScudo', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/matteo-ciciani/scudo/issues
On BioConductor:rScudo-1.21.0(bioc 3.20)rScudo-1.20.0(bioc 3.19)
Last updated 2 months agofrom:f66cee90ad
Exports:consensusDownSignaturesconsensusUpSignaturesdistMatrixdownSignaturesgroupsAnnotationscudoClassifyscudoCytoscapescudoModelscudoNetworkscudoParamsscudoPlotScudoResultsscudoTestscudoTrainselectedFeaturesupSignatures
Dependencies:abindaskpassBiobaseBiocGenericsclicpp11crayoncurlDelayedArrayGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrigraphIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpkgconfigR6rlangS4ArraysS4VectorsSparseArraystringistringrSummarizedExperimentsysUCSC.utilsvctrsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Signature-based Clustering for Diagnostic Purposes | rScudo-package |
| Performes classification using SCUDO | scudoClassify |
| Create a Cytoscape network from the output of scudoNetwork | scudoCytoscape |
| Generate model for 'caret::train' | scudoModel |
| Create graph from a ScudoResults object | scudoNetwork scudoNetwork,ScudoResults-method |
| Plot scudoNetwork result | scudoPlot |
| Class ScudoResults | consensusDownSignatures consensusDownSignatures,ScudoResults-method consensusUpSignatures consensusUpSignatures,ScudoResults-method distMatrix distMatrix,ScudoResults-method downSignatures downSignatures,ScudoResults-method groupsAnnotation groupsAnnotation,ScudoResults-method scudoParams scudoParams,ScudoResults-method ScudoResults ScudoResults-class selectedFeatures selectedFeatures,ScudoResults-method show,ScudoResults-method upSignatures upSignatures,ScudoResults-method |
| Performs SCUDO analysis on test dataset | scudoTest |
| Performs SCUDO analysis | scudoTrain |
