GeneRegionScan
This is the released version of GeneRegionScan; for the devel version, see GeneRegionScan.
GeneRegionScan
Bioconductor version: Release (3.23)
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("GeneRegionScan")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | R Script | |
| Reference Manual |
Details
| biocViews | DataImport, Microarray, OneChannel, SNP, Software, Visualization |
| Version | 1.68.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) (17.5 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_1.68.0.tar.gz |
| Windows Binary (x86_64) | GeneRegionScan_1.68.0.zip |
| macOS Binary (big-sur-x86_64) | GeneRegionScan_1.68.0.tgz |
| macOS Binary (sonoma-arm64) | GeneRegionScan_1.68.0.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 |