Package: SimBindProfiles
Title: Similar Binding Profiles
Version: 1.10.0
Date: 2013-09-17
Author: Bettina Fischer, Enrico Ferrero, Robert Stojnic, Steve Russell
Maintainer: Bettina Fischer <bef22@cam.ac.uk>
Description: SimBindProfiles identifies common and unique binding regions in genome tiling array data.
This package does not rely on peak calling, but directly compares binding profiles
processed on the same array platform. It implements a simple threshold approach,
thus allowing retrieval of commonly and differentially bound regions between
datasets as well as events of compensation and increased binding.
Depends: R (>= 2.10), methods, Ringo
Imports: limma, mclust, Biobase
biocViews: Microarray, Software
License: GPL-3
NeedsCompilation: no
Packaged: 2016-05-04 05:06:44 UTC; biocbuild
Package: Starr
Version: 1.28.0
Date: 2009-10-12
Title: Simple tiling array analysis of Affymetrix ChIP-chip data
Author: Benedikt Zacher, Johannes Soeding, Pei Fen Kuan, Matthias Siebert, Achim Tresch
Maintainer: Benedikt Zacher <zacher@lmb.uni-muenchen.de>
Depends: Ringo, affy, affxparser
Imports: pspline, MASS, zlibbioc
Description: 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.
License: Artistic-2.0
biocViews:
Microarray,OneChannel,DataImport,QualityControl,Preprocessing,ChIPchip
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2016-05-04 03:16:03 UTC; biocbuild
Package: ccTutorial
Type: Package
Title: Data package for ChIP-chip tutorial
Version: 1.10.0
Date: 2009-09-14
Author: Joern Toedling, Wolfgang Huber
Maintainer: Joern Toedling <joern.toedling@curie.fr>
Depends: R (>= 2.10), Ringo (>= 1.9.8), affy (>= 1.23.4), topGO (>=
1.13.1)
Imports: Biobase
Suggests: biomaRt, Biobase (>= 2.5.5), xtable
Description: This is a data package that accompanies a ChIP-chip
tutorial, which has been published in PLoS Computational Biology.
The data and source code in this package allow the reader to
completely reproduce the steps in the tutorial.
References: Joern Toedling and Wolfgang Huber (2008) Analyzing
ChIP-chip Data Using Bioconductor. PLoS Computational Biology,
4(11):e1000227.
License: Artistic-2.0
biocViews: ExperimentData, Mus_musculus_Data, MicroarrayData,
ChipOnChipData
NeedsCompilation: no
Packaged: 2016-05-07 20:16:08 UTC; biocbuild
providing 
.