GeneRegionScan

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see GeneRegionScan.

GeneRegionScan


Bioconductor version: 3.7

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 "3.5") 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 1.36.0
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
URL
See More
Suggests BSgenome, affy, AnnotationDbi
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package GeneRegionScan_1.36.0.tar.gz
Windows Binary GeneRegionScan_1.36.0.zip
Mac OS X 10.11 (El Capitan) GeneRegionScan_1.36.0.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
Old Source Packages for BioC 3.7 Source Archive