Package: tilingArray
Version: 1.87.0
Title: Transcript mapping with high-density oligonucleotide tiling
        arrays
Author: Wolfgang Huber, Zhenyu Xu, Joern Toedling with contributions from Matt Ritchie
Maintainer: Zhenyu Xu <zxu@embl.de>
Depends: R (>= 2.11.0), Biobase, methods, pixmap
Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4
Suggests:
Description: The package provides functionality that can be
	useful for the analysis of high-density tiling microarray data (such
	as from Affymetrix genechips) for measuring transcript abundance and
	architecture. The main functionalities of the package are: 1. the class
	'segmentation' for representing partitionings of a linear series of
	data; 2. the function 'segment' for fitting piecewise constant models
	using a dynamic programming algorithm that is both fast and exact; 3.
	the function 'confint' for calculating confidence intervals using the
	strucchange package; 4. the function 'plotAlongChrom' for generating
	pretty plots; 5. 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: Artistic-2.0
Collate: AllClasses.R AllGenerics.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 raster.image.R plotSegmentationDots.R
        plotSegmentationHeatmap.R PMindex.R methods-segmentation.R
        zzz.R
LazyLoad: Yes
biocViews: Microarray, OneChannel, Preprocessing, Visualization
git_url: https://git.bioconductor.org/packages/tilingArray
git_branch: devel
git_last_commit: b4f53ec
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: yes
Packaged: 2025-06-05 02:36:01 UTC; biocbuild
Built: R 4.5.0; x86_64-w64-mingw32; 2025-06-05 14:13:03 UTC; windows
Archs: x64
