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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("simpleaffy")
In most cases, you don't need to download the package archive at all.
simpleaffy
Very simple high level analysis of Affymetrix data
Bioconductor version: 2.14
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>
Citation (from within R,
enter citation("simpleaffy")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("simpleaffy")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("simpleaffy")
| R Script | simpleaffy primer | |
| Reference Manual | ||
| Text | README |
Details
| biocViews | Annotation, DataImport, DifferentialExpression, Microarray, OneChannel, Preprocessing, QualityControl, ReportWriting, Software, Transcription, Visualization |
| Version | 2.40.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier |
| 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 |
| Suggests | |
| System Requirements | |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | simpleaffy_2.40.0.tar.gz |
| Windows Binary | simpleaffy_2.40.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | simpleaffy_2.40.0.tgz |
| Mac OS X 10.9 (Mavericks) | simpleaffy_2.40.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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