ArrayTools

DOI: 10.18129/B9.bioc.ArrayTools    

This package is for version 3.9 of Bioconductor; for the 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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF	R Script	1. Primer
PDF		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) (11 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
Links To Me
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
Package Short Url	https://bioconductor.org/packages/ArrayTools/
Package Downloads Report	Download Stats