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Jianping Hua, D. Craig, M. Brun, J. Webster, V. Zismann, Waibhav Tembe, K. Joshipura, M. Huentelman, E. Dougherty, D. Stephan (2006)
Genetics and population analysis SNiPer-HD : improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays
(2009)
R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips
Wei Shi, A. Banerjee, Matthew Ritchie, S. Gerondakis, G. Smyth (2009)
Illumina WG-6 BeadChip strips should be normalized separatelyBMC Bioinformatics, 10
BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btm311 Genome analysis beadarray: R classes and methods for Illumina bead-based data
License: CC BY-NC
E. Giannoulatou, C. Yau, S. Colella, J. Ragoussis, C. Holmes (2008)
GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference populationBioinformatics, 24 19
S. Grant, H. Hakonarson (2008)
Microarray technology and applications in the arena of genome-wide association.Clinical chemistry, 54 7
N. Rabbee, Terence Speed (2006)
A genotype calling algorithm for affymetrix SNP arraysBioinformatics, 22 1
K. Gunderson, F. Steemers, Grace Lee, L. Mendoza, M. Chee (2005)
A genome-wide scalable SNP genotyping assay using microarray technologyNature Genetics, 37
(2007)
beadarray: R classes and methods for Illumina bead-based dataBioinformatics, 23
Jonathan Cairns, M. Dunning, Matthew Ritchie, R. Russell, A. Lynch (2008)
BASH: a tool for managing BeadArray spatial artefactsBioinformatics, 24
J. Staaf, J. Vallon-Christersson, D. Lindgren, G. Juliusson, R. Rosenquist, M. Höglund, Å. Borg, M. Ringnér (2008)
Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratiosBMC Bioinformatics, 9
B. Carvalho, H. Bengtsson, T. Speed, R. Irizarry (2006)
Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data.Biostatistics, 8 2
(2007)
SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arraysBioinformatics, 23
R. Gentleman, V. Carey, D. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Yongchao Ge, Jeff Gentry, K. Hornik, T. Hothorn, W. Huber, S. Iacus, R. Irizarry, F. Leisch, Cheng Li, M. Maechler, A. Rossini, G. Sawitzki, Colin Smith, Gordon Smyth, L. Tierney, J. Yang, Jianhua Zhang (2004)
Bioconductor: open software development for computational biology and bioinformaticsGenome Biology, 5
Y. Teo, M. Inouye, K. Small, R. Gwilliam, P. Deloukas, D. Kwiatkowski, T. Clark (2007)
A genotype calling algorithm for the Illumina BeadArray platformBioinformatics, 23 20
K. Frazer, D. Ballinger, D. Cox, D. Hinds, L. Stuve, R. Gibbs, J. Belmont, A. Boudreau, P. Hardenbol, S. Leal, S. Pasternak, D. Wheeler, T. Willis, F. Yu, Huanming Yang, Changqing Zeng, Yang Gao, Haoran Hu, Weitao Hu, Chaohua Li, Wei Lin, Siqi Liu, Hao Pan, Xiaoli Tang, Jian Wang, Wei Wang, Jun Yu, Bo Zhang, Qingrun Zhang, Hongbin Zhao, Hui-Ping Zhao, Jun Zhou, S. Gabriel, Rachel Barry, B. Blumenstiel, Amy Camargo, M. Defelice, M. Faggart, Marie-Anne Goyette, Supriya Gupta, Jamie Moore, Huy Nguyen, R. Onofrio, Melissa Parkin, J. Roy, E. Stahl, E. Winchester, L. Ziaugra, D. Altshuler, Yan Shen, Zhijian Yao, Wei Huang, X. Chu, Yungang He, Li Jin, Yangfan Liu, Yayun Shen, Weiwei Sun, Haifeng Wang, Yi Wang, Ying Wang, Xiao-yan Xiong, Liang Xu, M. Waye, S. Tsui, H. Xue, J. Wong, L. Galver, Jian-Bing Fan, K. Gunderson, S. Murray, A. Oliphant, M. Chee, A. Montpetit, F. Chagnon, Vincent Ferretti, M. Leboeuf, J. Olivier, M. Phillips, Stéphanie Roumy, C. Sallée, A. Verner, T. Hudson, P. Kwok, Dongmei Cai, D. Koboldt, Raymond Miller, L. Pawlikowska, P. Taillon-Miller, M. Xiao, L. Tsui, W. Mak, You-Qiang Song, P. Tam, Yusuke Nakamura, T. Kawaguchi, T. Kitamoto, Takashi Morizono, A. Nagashima, Y. Ohnishi, A. Sekine, Toshihiro Tanaka, T. Tsunoda, P. Deloukas, C. Bird, Marcos Delgado, E. Dermitzakis, R. Gwilliam, S. Hunt, J. Morrison, Don Powell, B. Stranger, P. Whittaker, D. Bentley, M. Daly, P. Bakker, J. Barrett, Y. Chretien, J. Maller, S. Mccarroll, N. Patterson, I. Pe’er, A. Price, S. Purcell, D. Richter, Pardis Sabeti, R. Saxena, S. Schaffner, P. Sham, P. Varilly, Lincoln Stein, Lalitha Krishnan, A. Smith, M. Tello-Ruiz, Gudmundur Thorisson, A. Chakravarti, Peter Chen, D. Cutler, C. Kashuk, Shin Lin, G. Abecasis, W. Guan, Yun Li, Heather Munro, Zhaohui Qin, D. Thomas, G. McVean, A. Auton, L. Bottolo, Niall Cardin, S. Eyheramendy, C. Freeman, J. Marchini, S. Myers, C. Spencer, M. Stephens, P. Donnelly, L. Cardon, G. Clarke, David Evans, A. Morris, B. Weir, J. Mullikin, S. Sherry, M. Feolo, Andrew Skol, Houcan Zhang, I. Matsuda, Y. Fukushima, D. Macer, Eiko Suda, C. Rotimi, C. Adebamowo, I. Ajayi, Toyin Aniagwu, P. Marshall, C. Nkwodimmah, C. Royal, M. Leppert, M. Dixon, A. Peiffer, Renzong Qiu, A. Kent, Kazuto Kato, N. Niikawa, I. Adewole, B. Knoppers, Morris Foster, E. Clayton, Jessica Watkin, D. Muzny, L. Nazareth, E. Sodergren, G. Weinstock, I. Yakub, B. Birren, R. Wilson, L. Fulton, J. Rogers, J. Burton, N. Carter, C. Clee, M. Griffiths, Matthew Jones, K. McLay, R. Plumb, M. Ross, S. Sims, D. Willey, Zhu Chen, Hua Han, L. Kang, M. Godbout, J. Wallenburg, P. L'Archevêque, G. Bellemare, Koji Saeki, Hongguang Wang, Daochang An, Hongbo Fu, Qing Li, Zhen Wang, Ren-hao Wang, A. Holden, L. Brooks, J. Mcewen, M. Guyer, V. Wang, Jane Peterson, Michael Shi, J. Spiegel, L. Sung, Lynn Zacharia, F. Collins, Karen Kennedy, Ruth Jamieson, J. Stewart (2007)
A second generation human haplotype map of over 3.1 million SNPsNature, 449
Yuanyuan Xiao, M. Segal, J. Yang, R. Yeh (2007)
A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarraysBioinformatics, 23 12
(2009)
R: a language and environment for statistical computingR Foundation for Statistical Computing
Pan Du, W. Kibbe, Simon Lin (2008)
lumi: a pipeline for processing Illumina microarrayBioinformatics, 24 13
F. Steemers, Weihua Chang, Grace Lee, D. Barker, Richard Shen, K. Gunderson (2005)
Whole-genome genotyping with the single-base extension assayNature Methods, 3
J. Oosting, E. Lips, R. Eijk, P. Eilers, K. Szuhai, C. Wijmenga, H. Morreau, T. Wezel (2007)
High-resolution copy number analysis of paraffin-embedded archival tissue using SNP BeadArrays.Genome research, 17 3
D. Peiffer, Jennie Le, F. Steemers, Weihua Chang, Tony Jenniges, Francisco Garcia, K. Haden, Jiangzheng Li, C. Shaw, J. Belmont, S. Cheung, Richard Shen, D. Barker, K. Gunderson (2006)
High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping.Genome research, 16 9
Shin Lin, B. Carvalho, D. Cutler, D. Arking, A. Chakravarti, R. Irizarry (2008)
Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarraysGenome Biology, 9
V. Galinsky (2003)
Automatic registration of microarray images. II. Hexagonal gridBioinformatics, 19 14
Summary: Illumina produces a number of microarray-based technologies for human genotyping. An Infinium BeadChip is a two-color platform that types between 105 and 106 single nucleotide polymorphisms (SNPs) per sample. Despite being widely used, there is a shortage of open source software to process the raw intensities from this platform into genotype calls. To this end, we have developed the R/Bioconductor package crlmm for analyzing BeadChip data. After careful preprocessing, our software applies the CRLMM algorithm to produce genotype calls, confidence scores and other quality metrics at both the SNP and sample levels. We provide access to the raw summary-level intensity data, allowing users to develop their own methods for genotype calling or copy number analysis if they wish.Availability and Implementation: The crlmm Bioconductor package is available from http://www.bioconductor.org. Data packages and documentation are available from http://rafalab.jhsph.edu/software.html.Contact: mritchie@wehi.edu.au; rafa@jhu.edu
Bioinformatics – Oxford University Press
Published: Aug 6, 2009
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