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Package: tilingArray
Version: 1.50.0
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
NeedsCompilation: yes
Packaged: 2016-05-04 02:44:24 UTC; biocbuild
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providing 
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