GeneRegionScan

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see GeneRegionScan.

GeneRegionScan


Bioconductor version: 3.9

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 <lasfol at cbs.dtu.dk>

Citation (from within R, enter citation("GeneRegionScan")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GeneRegionScan")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("GeneRegionScan")
GeneRegionScan PDF R Script
Reference Manual PDF

Details

biocViews DataImport, Microarray, OneChannel, SNP, Software, Visualization
Version 1.40.0
In Bioconductor since BioC 2.4 (R-2.9) (15 years)
License GPL (>= 2)
Depends methods, Biobase(>= 2.5.5), Biostrings
Imports S4Vectors(>= 0.9.25), Biobase(>= 2.5.5), affxparser, RColorBrewer, Biostrings
System Requirements
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Suggests BSgenome, affy, AnnotationDbi
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Package Archives

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

Source Package GeneRegionScan_1.40.0.tar.gz
Windows Binary GeneRegionScan_1.40.0.zip
Mac OS X 10.11 (El Capitan) GeneRegionScan_1.40.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GeneRegionScan
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GeneRegionScan
Bioc Package Browser https://code.bioconductor.org/browse/GeneRegionScan/
Package Short Url https://bioconductor.org/packages/GeneRegionScan/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive