simpleaffy

DOI: 10.18129/B9.bioc.simpleaffy    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see simpleaffy.

Very simple high level analysis of Affymetrix data

Bioconductor version: 3.8

Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures...

Author: Crispin J Miller

Maintainer: Crispin Miller <cmiller at picr.man.ac.uk>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("simpleaffy")

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("simpleaffy")

 

PDF	R Script	simpleaffy primer
PDF		Reference Manual
Text		README

Details

biocViews	Annotation, DataImport, DifferentialExpression, Microarray, OneChannel, Preprocessing, QualityControl, ReportWriting, Software, Transcription, Visualization
Version	2.58.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 14 years)
License	GPL (>= 2)
Depends	R (>= 2.0.0), methods, utils, grDevices, graphics, stats, BiocGenerics(>= 0.1.12), Biobase, affy(>= 1.33.6), genefilter, gcrma
Imports	methods, utils, grDevices, graphics, stats, BiocGenerics, Biobase, affy, genefilter, gcrma
LinkingTo
Suggests
SystemRequirements
Enhances
URL	http://www.bioconductor.org http://bioinformatics.picr.man.ac.uk/simpleaffy/
Depends On Me	yaqcaffy
Imports Me	affyQCReport, arrayMvout
Suggests Me	AffyExpress, ArrayTools, ELBOW
Links To Me
Build Report

Package Archives

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

Source Package	simpleaffy_2.58.0.tar.gz
Windows Binary	simpleaffy_2.58.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	simpleaffy_2.58.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/simpleaffy
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/simpleaffy
Package Short Url	http://bioconductor.org/packages/simpleaffy/
Package Downloads Report	Download Stats