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Copy Number Analysis

Parent category Analysis
Description ArrayCGH data analysis
Component Version Inputs Outputs Description
ACGHnorm 1.4 caseIn, control, admixtureMatrix, probeAnnotation casechannel, controlchannel, fit Normalizes two channel array CGH data with LOESS, median or mode.
ACGHsegment 2.0 caseChan, geneAnnotation report, segments, tholds, lossProbs, gainProbs, normProbs, rawSegments, frequency Segments Array CGH data with the Circular Binary Segmentation (CBS) algorithm and produces hard or soft copy number aberration calls.
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.
CNACaller 1.0 segments, probeAnnotation regions Calls significant copy number alterations from a group of segmented copy number alteration profiles.
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.
RUBIC 1.0 segments, markers, genes gains, losses, plots RUBIC detects recurrent copy number aberrations using copy number breaks, rather than recurrently amplified or deleted regions.
SegmentPlot 1.5 chrSegments plot, SignRegion Plots segmented chromosomal data.

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