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

segmentSeq

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

Bioconductor version: 2.13

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>

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("segmentSeq")

 

PDF	R Script	methylationAnalysis
PDF	R Script	segmentSeq
PDF		Reference Manual

Details

biocViews	Bioinformatics, HighThroughputSequencing, MultipleComparisons, Software
Version	1.14.0
In Bioconductor since	BioC 2.6 (R-2.11)
License	GPL-3
Depends	R (>= 2.3.0), methods, baySeq(>= 1.15.4), ShortRead, GenomicRanges, IRanges
Imports	baySeq, graphics, grDevices, IRanges, methods, utils, GenomicRanges
Suggests	snow
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	segmentSeq_1.14.0.tar.gz
Windows Binary	segmentSeq_1.14.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	segmentSeq_1.14.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats