Starr

DOI: 10.18129/B9.bioc.Starr    

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

Simple tiling array analysis of Affymetrix ChIP-chip data

Bioconductor version: 3.8

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 "3.5") 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

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	1.38.0
In Bioconductor since	BioC 2.5 (R-2.10) (9.5 years)
License	Artistic-2.0
Depends	Ringo, affy, affxparser
Imports	pspline, MASS, zlibbioc
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Depends On Me
Imports Me
Suggests Me	nucleR
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Build Report

Package Archives

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

Source Package	Starr_1.38.0.tar.gz
Windows Binary	Starr_1.38.0.zip
Mac OS X 10.11 (El Capitan)	Starr_1.38.0.tgz
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	http://bioconductor.org/packages/Starr/
Package Downloads Report	Download Stats