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Parent category Analysis
Description Exon and gene expression data integration with other data
Component Version Inputs Outputs Description
CN2GECollection 1.0 exprMatrix, cnaMatrix, exprAnnotation, exprRefMatrix, cnaRefMatrix, labels concomitantGenes, concomitantGenes2, plot Encapsulates three algorithms with similar inputs for copy number to RNA expression integration.
CNGEIntegrator 1.1.0 CNAProbLoss, CNAProbGain, CNAProbNorm, exprMatrix, exprAnnotation integrationResult Performs one of two possible nonparametric tests for the detection of copy number induced differential gene expression.
DataOverlap 1.0 annot1, annot2 annot Take the union of and collapse 2 datasets, with the option to filter out rows with NAs.
ExpExpIntegration 1.1 labelMatrix, exprMatrix Values Integrates gene/transcript/other expression data with binary explanatory data derived in some way.
ExprMethylCGH 1.1.1 exprMatrix, cghMatrix, methylMatrix statistics Integrates expression data with methylation and CGH data by using two label matrices of ones and zeros.
GlobalCorrelation 1.2 gene, mirna correlated_filtered, correlated_all, expression_miRNA, expression_mRNA Compute correlation between miRNA and gene/transcript expression.
GSVDIntegrator 1.0.1 exprMatrix, cnaMatrix, exprAnnotation integrationResults, cghResults, annotations Extracts variation patterns from two matrices based on the generalized singular value decomposition.
MirMatch 1.0 utrSeeds, matureSeq, pairs matched String match for between mature miRNA seeds and target UTR seeds.
TPquery 0.3 refTable array, annot Retrieve target prediction and target validated data from an SQLite database to annotate a list of miRNAs or a list of miRNA-target gene pairs.

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