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source("http://bioconductor.org/biocLite.R")
biocLite("ArrayTools")

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ArrayTools

 

geneChip Analysis Package

Bioconductor version: Release (3.1)

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 (from within R, enter citation("ArrayTools")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("ArrayTools")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ArrayTools")

 

PDF R Script 1. Primer
PDF   Reference Manual

Details

biocViews Annotation, DifferentialExpression, Microarray, OneChannel, Preprocessing, QualityControl, ReportWriting, Software, StatisticalMethod, Visualization
Version 1.28.0
In Bioconductor since BioC 2.3 (R-2.8) (6.5 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
LinkingTo
Suggests simpleaffy, R2HTML, affydata, affyPLM, genefilter, annaffy, gcrma, hugene10sttranscriptcluster.db
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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Package Source ArrayTools_1.28.0.tar.gz
Windows Binary ArrayTools_1.28.0.zip
Mac OS X 10.6 (Snow Leopard) ArrayTools_1.28.0.tgz
Mac OS X 10.9 (Mavericks) ArrayTools_1.28.0.tgz
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