GeneRegionScan

GeneRegionScan

Bioconductor version: 2.8

A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.

Author: Lasse Folkersen, Diego Diez

Maintainer: Lasse Folkersen <lasse.folkersen at ki.se>

To install this package, start R and enter:

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

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

    citation("GeneRegionScan")

Documentation

PDF R Script GeneRegionScan
PDF   Reference Manual

Details

biocViews Microarray, DataImport, SNP, OneChannel, Visualization
Depends methods, Biobase(>= 2.5.5), Biostrings
Imports Biobase(>= 2.5.5), affxparser, RColorBrewer, Biostrings
Suggests BSgenome, affy, AnnotationDbi
System Requirements
License GPL (>= 2)
URL
Depends On Me
Imports Me
Suggests Me
Version 1.8.0
Since Bioconductor 2.4 (R-2.9)

Package Downloads

Package Source GeneRegionScan_1.8.0.tar.gz
Windows Binary GeneRegionScan_1.8.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary GeneRegionScan_1.8.0.tgz
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