Starr

Simple tiling array analysis of Affymetrix ChIP-chip data

Bioconductor version: Release (2.7)

Starr facilitates the analysis of ChIP-chip data, in particular that of Affymetrix tiling arrays. The package provides functions for data import, quality assessment, data visualization and exploration. Furthermore, it includes high-level analysis features like association of ChIP signals with annotated features, correlation analysis of ChIP signals and other genomic data (e.g. gene expression), peak-finding with the CMARRT algorithm and comparative display of multiple clusters of ChIP-profiles. It uses the basic Bioconductor classes ExpressionSet and probeAnno for maximum compatibility with other software on Bioconductor. All functions from Starr can be used to investigate preprocessed data from the Ringo package, and vice versa. An important novel tool is the the automated generation of correct, up-to-date microarray probe annotation (bpmap) files, which relies on an efficient mapping of short sequences (e.g. the probe sequences on a microarray) to an arbitrary genome.

Author: Benedikt Zacher, Johannes Soeding, Pei Fen Kuan, Matthias Siebert, Achim Tresch

Maintainer: Benedikt Zacher

To install this package, start R and enter:

source("http:///biocLite.R")
biocLite("Starr")    

Documentation

PDF

R Script

Simple tiling array analysis

Reference Manual

Details

biocViews	Microarray, OneChannel, DataImport, QualityControl, Preprocessing, ChIPchip
Depends	Ringo, affy, affxparser
Imports	pspline, MASS
Suggests
System Requirements
License	Artistic-2.0
URL
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Version	1.6.0

Package Downloads

Package Source	Starr_1.6.0.tar.gz
Windows Binary	Starr_1.6.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	Starr_1.6.0.tgz
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