affycoretools

DOI: 10.18129/B9.bioc.affycoretools  

Functions useful for those doing repetitive analyses with Affymetrix GeneChips

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Creating annotated output with \Biocpkg{affycoretools} and ReportingTools
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, Microarray, OneChannel, ReportWriting, Software
Version	1.70.0
In Bioconductor since	BioC 1.8 (R-2.3) (17 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
LinkingTo
Suggests	affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me	AgiMicroRna
Imports Me
Suggests Me	EnMCB
Links To Me
Build Report

Package Archives

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

Source Package	affycoretools_1.70.0.tar.gz
Windows Binary	affycoretools_1.70.0.zip
macOS Binary (x86_64)	affycoretools_1.70.0.tgz
macOS Binary (arm64)	affycoretools_1.70.0.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