| 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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Integration