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CAFE attempts to find chromosomal aberrations in microarray expression (mRNA) data. It contains several plotting functions to aid in visualizing these aberrations. It generally recapitulates the workflow described by Mayshar et al (see references), and implements several algorithms described by Friedrich et al (see references).
● Data Source:
BioConductor
● Keywords: package
● Alias: CAFE, CAFE-package
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Normalizes and computes relative expressions for all CEL files in work directory
● Data Source:
BioConductor
● Keywords: datagen
● Alias: ProcessCels
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Calculate significant chromosomal arms with various statistical tests
● Data Source:
BioConductor
● Keywords: multivariate
● Alias: armStats
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Calculate significant chromosome bands with various statistical tests
● Data Source:
BioConductor
● Keywords: multivariate
● Alias: bandStats
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Calculate significant chromosomes with various statistical tests
● Data Source:
BioConductor
● Keywords: multivariate
● Alias: chromosomeStats
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Provides command line interface for subsetting input datasets
● Data Source:
BioConductor
● Keywords: manip
● Alias: cliSubset
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Plots chromosome plots with a discontinuous smoother
● Data Source:
BioConductor
● Keywords: dplot, hplot
● Alias: discontPlot
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Calculates discontinuous smoother
● Data Source:
BioConductor
● Keywords: smooth
● Alias: discontSmooth
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Plots all chromosomes in horizontal alignment next to each other, with optionally a moving average smoother applied to the data
● Data Source:
BioConductor
● Keywords: dplot, hplot
● Alias: facetPlot
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Combines pvalues by using Fisher's method
● Data Source:
BioConductor
● Keywords: htest
● Alias: fisher.method
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providing 
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