To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

Starr

This is the development version of Starr; for the stable release version, see Starr.

Simple tiling array analysis of Affymetrix ChIP-chip data

Bioconductor version: Development (3.0)

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 <zacher at lmb.uni-muenchen.de>

To install this package, start R and enter:

Citation (from within R, enter citation("Starr")):

Installation

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Starr")

 

PDF R Script Simple tiling array analysis
PDF   Reference Manual

Details

biocViews ChIPchip, DataImport, Microarray, OneChannel, Preprocessing, QualityControl, Software
Version 1.21.0
In Bioconductor since BioC 2.5 (R-2.10)
License Artistic-2.0
Depends Ringo, affy, affxparser
Imports pspline, MASS, zlibbioc
Suggests
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source Starr_1.21.0.tar.gz
Windows Binary Starr_1.21.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) Starr_1.21.0.tgz
Mac OS X 10.9 (Mavericks) Starr_1.21.0.tgz
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