affycoretools

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see affycoretools.

Functions useful for those doing repetitive analyses with Affymetrix GeneChips


Bioconductor version: 3.11

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")):

Installation

To install this package, start R (version "4.0") 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 Manual PDF
NEWS Text

Details

biocViews GeneExpression, Microarray, OneChannel, ReportWriting, Software
Version 1.60.1
In Bioconductor since BioC 1.8 (R-2.3) (18 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

Package Archives

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

Source Package affycoretools_1.60.1.tar.gz
Windows Binary affycoretools_1.60.1.zip
macOS 10.13 (High Sierra) affycoretools_1.60.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/affycoretools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/affycoretools
Bioc Package Browser https://code.bioconductor.org/browse/affycoretools/
Package Short Url https://bioconductor.org/packages/affycoretools/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive