GeneRegionScan

DOI: 10.18129/B9.bioc.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>

Installation

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

if (!requireNamespace("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")

 

PDF	R Script	GeneRegionScan
PDF		Reference Manual

Details

biocViews	DataImport, Microarray, OneChannel, SNP, Software, Visualization
Version	1.40.0
In Bioconductor since	BioC 2.4 (R-2.9) (10.5 years)
License	GPL (>= 2)
Depends	methods, Biobase(>= 2.5.5), Biostrings
Imports	S4Vectors(>= 0.9.25), Biobase(>= 2.5.5), affxparser, RColorBrewer, Biostrings
LinkingTo
Suggests	BSgenome, affy, AnnotationDbi
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

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
Package Short Url	https://bioconductor.org/packages/GeneRegionScan/
Package Downloads Report	Download Stats