Starr

DOI: 10.18129/B9.bioc.Starr    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see Starr.

Simple tiling array analysis of Affymetrix ChIP-chip data

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("Starr")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	ChIPchip, DataImport, Microarray, OneChannel, Preprocessing, QualityControl, Software
Version	1.46.0
In Bioconductor since	BioC 2.5 (R-2.10) (11.5 years)
License	Artistic-2.0
Depends	Ringo, affy, affxparser
Imports	pspline, MASS, zlibbioc
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Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/Starr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Starr
Package Short Url	https://bioconductor.org/packages/Starr/
Package Downloads Report	Download Stats