ArrayTools
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see ArrayTools.
geneChip Analysis Package
Bioconductor version: 3.9
This package is designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.
Author: Xiwei Wu, Arthur Li
Maintainer: Arthur Li <xueli at coh.org>
citation("ArrayTools")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ArrayTools")
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("ArrayTools")| 1. Primer | R Script | |
| Reference Manual |
Details
| biocViews | Annotation, DifferentialExpression, Microarray, OneChannel, Preprocessing, QualityControl, ReportWriting, Software, StatisticalMethod, Visualization |
| Version | 1.44.0 |
| In Bioconductor since | BioC 2.3 (R-2.8) (15.5 years) |
| License | LGPL (>= 2.0) |
| Depends | R (>= 2.7.0), affy(>= 1.23.4), Biobase(>= 2.5.5), methods |
| Imports | affy, Biobase, graphics, grDevices, limma, methods, stats, utils, xtable |
| System Requirements | |
| URL |
See More
| Suggests | simpleaffy, R2HTML, affydata, affyPLM, genefilter, annaffy, gcrma, hugene10sttranscriptcluster.db |
| 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 | ArrayTools_1.44.0.tar.gz |
| Windows Binary | ArrayTools_1.44.0.zip |
| Mac OS X 10.11 (El Capitan) | ArrayTools_1.44.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ArrayTools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ArrayTools |
| Bioc Package Browser | https://code.bioconductor.org/browse/ArrayTools/ |
| Package Short Url | https://bioconductor.org/packages/ArrayTools/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |