ArrayTools

This package is for version 3.7 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: 3.7

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 (version "3.5") 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 PDF R Script
Reference Manual PDF

Details

biocViews Annotation, DifferentialExpression, Microarray, OneChannel, Preprocessing, QualityControl, ReportWriting, Software, StatisticalMethod, Visualization
Version 1.40.0
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
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Suggests simpleaffy, R2HTML, affydata, affyPLM, genefilter, annaffy, gcrma, hugene10sttranscriptcluster.db
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Package Archives

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

Source Package ArrayTools_1.40.0.tar.gz
Windows Binary ArrayTools_1.40.0.zip
Mac OS X 10.11 (El Capitan) ArrayTools_1.40.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ArrayTools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ArrayTools
Package Short Url https://bioconductor.org/packages/ArrayTools/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive