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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GeneRegionScan")
In most cases, you don't need to download the package archive at all.
GeneRegionScan
GeneRegionScan
Bioconductor version: 3.0
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>
Citation (from within R,
enter citation("GeneRegionScan")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("GeneRegionScan")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GeneRegionScan")
| R Script | GeneRegionScan | |
| Reference Manual |
Details
| biocViews | DataImport, Microarray, OneChannel, SNP, Software, Visualization |
| Version | 1.22.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) |
| License | GPL (>= 2) |
| Depends | methods, Biobase(>= 2.5.5), Biostrings |
| Imports | Biobase(>= 2.5.5), affxparser, RColorBrewer, Biostrings |
| LinkingTo | |
| Suggests | BSgenome, affy, AnnotationDbi |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | GeneRegionScan_1.22.0.tar.gz |
| Windows Binary | GeneRegionScan_1.22.0.zip |
| Mac OS X 10.6 (Snow Leopard) | GeneRegionScan_1.22.0.tgz |
| Mac OS X 10.9 (Mavericks) | GeneRegionScan_1.22.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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