Package: tilingArray
Version: 1.16.0
Title: Analysis of high-density oligonucleotide tiling arrays
Author: Wolfgang Huber, Joern Toedling, Matt Ritchie
Maintainer: W. Huber <huber@ebi.ac.uk>
Depends: R (>= 2.6.0), methods, Biobase (>= 1.15.27), affy (>= 1.15.7), RColorBrewer (>= 0.2-3),
        grid (>= 2.0.0), strucchange (>= 1.3-0), 
        vsn (>= 3.0.11), genefilter (>= 1.15.10), geneplotter (>= 1.15.7), pixmap (>= 0.4-4)
Suggests:
Description: The package provides some functionalities that can be
	useful for the analysis of high-density tiling microarray data (such
	as Affymetrix genechips) for measuring transcript abundance and
	architecture. The main functionalities of the package are: The class
	'segmentation' for representing partitionings of a linear series of
	data. The functions 'segment' for fitting piecewise constant models
	using a dynamic programming algorithm that is both fast and exact, and
	'confint' for calculating confidence intervals using the strucchange
	package. The function 'plotAlongChrom' for generating pretty
	plots. The function 'normalizeByReference' for probe-sequence
	dependent response adjustment from a (set of) reference
	hybridizations.
Reference: Huber W, Toedling J, Steinmetz, L. Transcript mapping with high-density 
	oligonucleotide tiling arrays. Bioinformatics 22, 1963-1970 (2006).
License: The Artistic License, Version 2.0
Collate: AllClasses.R AllGeneric.R
	 normalizeByReference.R posMin.R otherStrand.R qcPlots.R
	 comparisonPlot.R plotAlongChromLegend.R readCel2eSet.R
	 confint.segmentation.R plotAlongChrom.R sampleStep.R
	 costMatrix.R plotPenLL.R segChrom.R
	 findsegments.R  grid.image.R 
	 plotSegmentationDots.R plotSegmentationHeatmap.R
	 PMindex.R methods-segmentation.R
	 zzz.R
LazyLoad: Yes
biocViews: Microarray, OneChannel, Preprocessing, Visualization
Packaged: Wed Oct  3 14:21:14 2007; biocbuild
