Package: segmentSeq
Type: Package
Title: Takes high-throughput sequencing data and uses it to define
        segments of the genome to which a high density of reads align.
Version: 1.0.1
Date: 2010-01-20
Author: Thomas J. Hardcastle
Maintainer: Thomas J. Hardcastle <tjh48@cam.ac.uk>
Description: High-throughput sequencing technologies allow the
        production of large volumes of short sequences, which can be
        aligned to the genome to create a set of matches to the genome.
        By looking for regions of the genome which to which there are
        high densities of matches, we can infer a segmentation of the
        genome into regions of biological significance. The methods in
        this package allow the simultaneous segmentation of data from
        multiple samples, taking into account replicate data, in order
        to create a consensus segmentation. This has obvious
        applications in a number of classes of sequencing experiments,
        particularly in the discovery of small RNA loci and novel mRNA
        transcriptome discovery.
License: GPL-3
LazyLoad: yes
Depends: R (>= 2.3.0), methods, baySeq (>= 1.1.23), ShortRead
Suggests: snow
Imports: baySeq, graphics, grDevices, IRanges, methods, utils
Collate: AllClasses.R segData-accessors.R alignmentData-accessors.R
        getCounts.R plotGenome.R processAD.R processTags.R
        segmentSequences.R getPriors.R filterSegments.R
biocViews: Bioinformatics, HighThroughputSequencing,
        MultipleComparisons
Packaged: 2010-05-04 23:24:15 UTC; biocbuild
Built: R 2.11.0; ; 2010-05-05 04:48:23 UTC; windows
