Bioconductor Developer Survey 2026 Now Open!

affycoretools

This is the released version of affycoretools; for the devel version, see affycoretools.

All versions 3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

Functions useful for those doing repetitive analyses with Affymetrix GeneChips


Bioconductor version: Release (3.23)

Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.

Author: James W. MacDonald

Maintainer: James W. MacDonald <jmacdon at u.washington.edu>

Citation (from within R, enter citation("affycoretools")):

James W. MacDonald. affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips. doi:10.18129/B9.bioc.affycoretools, R package version 1.84.0, https://bioconductor.org/packages/affycoretools.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("affycoretools")

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("affycoretools")
Creating annotated output with \Biocpkg{affycoretools} and ReportingTools HTML R Script
Reference ManualPDF
NEWSText

Details

biocViews GeneExpression, Microarray, OneChannel, ReportWriting, Software
Version1.84.0
In Bioconductor sinceBioC 1.8 (R-2.3) (20.5 years)
License Artistic-2.0
Depends Biobase, methods
Imports affy, limma, GOstats, gcrma, splines, xtable, AnnotationDbi, ggplot2, gplots, oligoClasses, ReportingTools, hwriter, lattice, S4Vectors, edgeR, RSQLite, BiocGenerics, DBI, Glimma
System Requirements
URL
See More
Suggests affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl, rmarkdown
Linking To
Enhances
Depends On Me AgiMicroRna
Imports Me
Suggests Me EnMCB
Links To Me
Build Report Build Report, r-universe

Package Archives

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

Source Package affycoretools_1.84.0.tar.gz
Windows Binary (x86_64) affycoretools_1.84.0.zip
macOS Binary (big-sur-x86_64) affycoretools_1.84.0.tgz
macOS Binary (sonoma-arm64) affycoretools_1.84.0.tgz
Source Repositorygit clone https://git.bioconductor.org/packages/affycoretools
Source Repository (Developer Access)git clone git@git.bioconductor.org:packages/affycoretools
Package Short Url https://bioconductor.org/packages/affycoretools/
Package Downloads ReportDownload Stats