Package: tilingArray
Version: 1.89.0
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
Config/pak/sysreqs: libpng-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 13:56:07 UTC
RemoteUrl: https://github.com/bioc/tilingArray
RemoteRef: HEAD
RemoteSha: 1959cebc6db93a9c8400f840156d92d878cd19ab
NeedsCompilation: yes
Packaged: 2025-10-30 13:42:56 UTC; root
Built: R 4.6.0; x86_64-w64-mingw32; 2025-10-30 13:44:47 UTC; windows
Archs: x64
