segmentSeq

Methods for identifying small RNA loci from high-throughput sequencing data

Bioconductor version: 2.8

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.

Author: Thomas J. Hardcastle

Maintainer: Thomas J. Hardcastle <tjh48 at cam.ac.uk>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("segmentSeq")

To cite this package in a publication, start R and enter:

    citation("segmentSeq")

Documentation

PDF R Script segmentSeq
PDF   Reference Manual

Details

biocViews Bioinformatics, HighThroughputSequencing, MultipleComparisons
Depends R (>= 2.3.0), methods, baySeq(>= 1.1.23), ShortRead
Imports baySeq, graphics, grDevices, IRanges, methods, utils
Suggests snow
System Requirements
License GPL-3
URL
Depends On Me
Imports Me
Suggests Me
Version 1.4.0
Since Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source segmentSeq_1.4.0.tar.gz
Windows Binary segmentSeq_1.4.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary segmentSeq_1.4.0.tgz
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