Software

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Gene and pathway-based GWAS

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Citation: Luo L, Peng G, Zhu Y, Dong H, Amos C, Xiong MM. (2010) Genome-wide gene and pathway analysis.  Eur J Hum Genet. 18:1045-1053

FPCA for association studies

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Citation: Luo L., Boerwinkle E., Xiong MM. (2011). Association studies for next-generation sequencing.

Genome-wide Interaction Analysis by Haplotype-based Odds-Ratio

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Citation: Wu X, Dong H, Luo L, Zhu Y, Peng G, Reveille JD, Xiong MM. (2010) A novel statistic for genome-wide interaction analysis. Plos Genetics. 6 (9), e1001131.

Manifold Learning for Human Population Structure Studies

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Citation: Siu H, Jin L, Xiong MM. (2012) Manifold Learning for Human Population Structure Studies. Plos Genetics. 7 (1), e29901.

Pedigree Analysis

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Citation: Zhu Y and Xiong MM. (2012) Family-Based Association Studies for Next-Generation Sequencing. Am J Human Genet. 90(6):1028-1045.

PB STAR

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Citation: Shugart YY, Zhu Y, Guo W, and Xiong MM. Weighted Pedigree-based Statistics for Testing the Association of Rare Variants. BMC Genomics, 13:667.

QTL(eQTL) Analysis for Next-generation sequencing

[Download] (file: FLM-Test.zip)
Citation: Luo L., Zhu Y., and Xiong MM. (2012) Quantitative Trait Locus (QTL) Analysis for Next-Generation Sequencing with the Functional Linear Models. J Medical Genetics. (In Press).

Smoothed Functional Principal Component Analysis

[Download] (File SFPCA.rar)
Citation: Luo L., Zhu Y., and Xiong MM.(2012) Penalized functional principal component analysis for sequence-based association studies. Eur J Hum Genet. 2012 Jul 11. doi: 10.1038/ejhg.2012.141. [Epub ahead of print]

R package of Canonical Correlation based RNA-Seq Co-expression Network

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Citation: Hong SJ., Chen XN, Jin L., and Xiong MM. Canonical Correlation Analysis for RNA-seq Co-expression Networks. Nucleic Acids Research. 2013.

Pathway-Association-NGS

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Citation: Zhao J., Zhu Y., Boerwinkle E., Xiong MM. (2013) Pathway Analysis with Next-Generation Sequencing Data. Submitted to Eur J Hum Genet.

FRG-Epistasis

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Citation: Zhang FT., Boerwinkle E., Xiong MM. (2013) Epistasis Analysis for Quantitative Trait with Next-generation Sequencing Data. Submitted to Genome Research.

Gene-gene Interaction for NGS

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Citation: Zhao JY, Zhu Y, and Xiong MM. (2013) Genome-wide Gene-gene Interaction Analysis for Next-generation Sequencing. Submitted to PLoS Genetics.

M-EPISTASIS

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Citation: Zhang F, Xie D, Liang M, Xiong M. (2016). Functional Regression Models for Epistasis Analysis of Multiple Quantitative Traits. PLoS Genet. 12(4):e1005965.

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Citation: Xu K, Jin L, Xiong M. (2017). Functional regression method for whole genome eQTL epistasis analysis with sequencing data. BMC Genomics. 18(1):385.

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Citation: Lin N, Zhu Y, Fan R and Xiong MM. (2016). A Quadratically Regularized Functional Canonical Correlation Analysis for Identifying the Global Structure of Pleiotropy with NGS Data. arXiv:1609.04902

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Citation: Lin N, Jiang J, Guo S, Xiong M. (2015). Functional Principal Component Analysis and Randomized Sparse Clustering Algorithm for Medical Image Analysis. PLoS One. 10(7):e0132945.