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Analysis of Affymetrix ChIP-chip data using starr and R/Bioconductor.

Zacher B, Torkler P, Tresch A. Zacher B, et al. Cold Spring Harb Protoc. 2011 May 1;2011(5):pdb.top110. doi: 10.1101/pdb.top110. Cold Spring Harb Protoc. 2011. PMID: 21536772

Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data.

Zacher B, Kuan PF, Tresch A. Zacher B, et al. BMC Bioinformatics. 2010 Apr 17;11:194. doi: 10.1186/1471-2105-11-194. BMC Bioinformatics. 2010. PMID: 20398407 Free PMC article.

rMAT--an R/Bioconductor package for analyzing ChIP-chip experiments.

Droit A, Cheung C, Gottardo R. Droit A, et al. Bioinformatics. 2010 Mar 1;26(5):678-9. doi: 10.1093/bioinformatics/btq023. Epub 2010 Jan 19. Bioinformatics. 2010. PMID: 20089513

ChIP-chip: data, model, and analysis.

Zheng M, Barrera LO, Ren B, Wu YN. Zheng M, et al. Biometrics. 2007 Sep;63(3):787-96. doi: 10.1111/j.1541-0420.2007.00768.x. Biometrics. 2007. PMID: 17825010

A physical model for tiling array analysis.

Chung HR, Kostka D, Vingron M. Chung HR, et al. Bioinformatics. 2007 Jul 1;23(13):i80-6. doi: 10.1093/bioinformatics/btm167. Bioinformatics. 2007. PMID: 17646349

Genome-wide mapping of protein-DNA interaction by chromatin immunoprecipitation and DNA microarray hybridization (ChIP-chip). Part B: ChIP-chip data analysis.

Göbel U, Reimer J, Turck F. Göbel U, et al. Methods Mol Biol. 2010;631:161-84. doi: 10.1007/978-1-60761-646-7_13. Methods Mol Biol. 2010. PMID: 20204875

ChIP-on-Chip Analysis methods for Affymetrix Tiling Arrays.

Yoder SJ, Enkemann SA. Yoder SJ, et al. Methods Mol Biol. 2009;523:367-81. doi: 10.1007/978-1-59745-190-1_24. Methods Mol Biol. 2009. PMID: 19381926

Genome-wide mapping of protein-DNA interaction by chromatin immunoprecipitation and DNA microarray hybridization (ChIP-chip). Part A: ChIP-chip molecular methods.

Reimer JJ, Turck F. Reimer JJ, et al. Methods Mol Biol. 2010;631:139-60. doi: 10.1007/978-1-60761-646-7_12. Methods Mol Biol. 2010. PMID: 20204874

Computational analysis of protein-DNA interactions from ChIP-seq data.

Rougemont J, Naef F. Rougemont J, et al. Methods Mol Biol. 2012;786:263-73. doi: 10.1007/978-1-61779-292-2_16. Methods Mol Biol. 2012. PMID: 21938632

[Finding targets of transcriptional regulators--chromatin immunoprecipitation assay (ChIP)].

Kus-Liśkiewicz M, Widłak W. Kus-Liśkiewicz M, et al. Postepy Biochem. 2011;57(4):418-24. Postepy Biochem. 2011. PMID: 22568174 Review. Polish.

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