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Brucker, Amanda, Shannon T. Holloway, and Jung-Ying Tzeng. CONCUR: Kernel-based association test for copy number variation (CNV) aggregate analysis (R)., 2020. |
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West, Rachel Marceau, and Shannon T. Holloway. POINT: Protein Structure Guided Local Test (R). 1.0 ed., 2019. |
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Zhu, Anqi, Joseph G. Ibrahim, and Michael I. Love. apeglm: Approximate posterior estimation for GLM coefficients (R)., 2018. |
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Jiang, Yuchao, and Nancy R. Zhang. CODEX2: Full-spectrum copy number variation detection by high-throughput DNA sequencing. (R)., 2018. |
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Lin, Jiaxing, Alexander Sibley, Tracy Truong, Kouros Owzar, and Zhiguo Li. groupedSurv: Efficient Estimation of Grouped Survival Models Using the Exact Likelihood Function (R). 1.0.0 ed., 2018. |
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Lin, Jiaxing, Yuan Wu, Xiaofei F. Wang, and Kouros Owzar. intcensROC: Fast Spline Function Based Constrained Maximum Likelihood Estimator for AUC Estimation of Interval Censored Survival Data (R). 0.1.1 ed., 2018. |
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Urrutia, Eugene, Hao Chen, Zilu Zhou, Nancy R. Zhang, and Yuchao Jiang. MARATHON: Integrates Multiple Related Statistical Software for Copy Number Profiling and Downstream Analyses (R)., 2018. |
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Liu, Yang, Wei Sun, and Qianchuan He. SAME: Somatic mutation Association test with Measurement Errors (R)., 2018. |
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Tao, Ran. TwoPhaseReg: Regression Analysis Under General Two-Phase Sampling (R)., 2018. |
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bcSeq: Fast Sequence Alignment for High-Throughput shRNA and CRISPR Screens (R)., 2017. |
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Gao, Fei, Donglin Zeng, and Dan-Yu Lin. PICAFT: Semiparametric Estimation of the Accelerated Failure Time Model With Partly Interval-Censored Data (R)., 2017. |
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Tang, Zheng-Zheng, Paul Bunn, Ran Tao, Z Liu, and Dan-Yu Lin. PreMeta: Facilitates the Exchange of Information Between Software Packages for Meta-Analysis (C++)., 2017. |
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Chen, Mengjie. SynthEx: Tools for CNA detection and tumor heterogeneity profiling (R)., 2017. |
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X Jeng, Jessie, Zhongyin John Daye, Wenbin Lu, and Jung-Ying Tzeng. AFNC: Adaptive false negative control (R)., 2016. |
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Wang, Xuefeng, Mengjie Chen, Xiaoqing Yu, Natapol Pornputtapong, Hao Chen, Nancy R. Zhang, Scott R Powers, and Michael Krauthammer. CLOSE: A toolkit for CNA/LOH analysis with Sequencing data., 2016. |
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Bunn, Paul, Donglin Zeng, and Dan-Yu Lin. IntCens: Nonparametric maximum likelihood estimation for a broad class of semiparametric regression models with general interval-censored data (R).., 2016. |
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Acharya, Chaitanya R., Janice M. McCarthy, Kouros Owzar, and Andrew S. Allen. JAGUAR: Joint analysis of genotype and group-specific variability using a novel score test approach to map expression quantitative trait loci (eQTL) (R). 3.0.1 ed., 2016. |
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Zhang, Chong, Yufeng Liu, and Shannon T. Holloway. RAMSVM: Reinforced angle-based multicategory support vector machines (R).. 2.0 ed., 2016. |
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Kimes, Patrick. sigclust2: Statistical Significance for Hierarchical Clustering (R). 1.2.4 ed., 2016. |
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Wang, WeiBo, Wei Wang, Wei Sun, James J. Crowley, and Jin P. Szatkiewicz. ASGENSENG: Detect Allele Specific CNV from Both WGS and WES Data (Python/Shell)., 2015. |
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Marceau, Rachel, Wenbin Lu, Michèle M. Sale, Bradford B. Worrall, Stephen R. Williams, Fang-Chi Hsu, Jung-Ying Tzeng, and Shannon T. Holloway. FastKM: A fast multiple-kernel method based on a low-rank approximation (R).. 1.0 ed., 2015. |
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Jiang, Yu, Yujun Han, Slavé Petrovski, Kouros Owzar, David B. Goldstein, and Andrew S. Allen. fitDNM: Test of de novo enrichment that incorporates functional information (R).. 1.0 ed., 2015. |
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Tao, Ran, Donglin Zeng, Nora Franceschini, Kari E. North, Eric Boerwinkle, and Dan-Yu Lin. MultiTDS: Analysis of Sequence Data Under Multivariate Trait-Dependent Sampling (C++)., 2015. |
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Hu, Yi-Juan, Yun Li, Paul L. Auer, and Dan-Yu Lin. SEQGWAS: Integrative analysis of sequencing and GWAS data (C/C++).. 1.0 ed., 2015. |
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Cao, Hongyuan, Mathew M. Churpek, Donglin Zeng, Jason P. Fine, and Shannon T. Holloway. SurvLong: Analysis of proportional hazards model with sparse longitudinal covariates (R).. 1.0 ed., 2015. |
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Cao, Hongyuan, Michael R. Kosorok, and Shannon T. Holloway. highTtest: Simultaneous critical values for t-tests in very high dimensions (R).. 1.0 ed., 2014. |
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Yi, Chanhee, Alexander Sibley, and Kouros Owzar. RSNPset: Genome-wide SNP set analysis on the basis of efficient scores (R).. v0.2 ed., 2014. |
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Lin, Dan-Yu, R Tao, W Kalsbeek, Donglin Zeng, Franklyn Gonzalez, Lindsay Fernández-Rhodes, Mariaelisa Graff, Gary G. Koch, Kari E. North, and Gerardo Heiss. SUGEN: Genetic Association Analysis Under Complex Survey Sampling (C++)., 2014. |
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Bondell, Howard D., and Shannon T. Holloway. CasANOVA: Simultaneous factor selection and collapsing levels in ANOVA (R).. R 3.0 ed., 2013. |
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Bondell, Howard D., Jung-Ying Tzeng, Megan L. Koehler, and Shannon T. Holloway. Haplo.CasGLM: Haplotype specific simultaneous factor selection and collapsing levels in GLM (R).. 3rd ed., 2013. |
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Chen, Guanhua, and Michael R. Kosorok. HSSVD: Biclustering with heterogeneous variance (R).., 2013. |
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Tang, Zheng-Zheng, and Dan-Yu Lin. MASS: Meta-analysis of sequencing studies (C).. 5.0 ed., 2013. |
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He, Qianchuan, and Dan-Yu Lin. MOST: Multivariate outcome score test (C).. 1.0 ed., 2013. |
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Lin, Dan-Yu, and Zheng-Zheng Tang. SCORE-Seq: Score tests for detecting disease associations with rare variants in sequencing studies (C).. 5.0 ed., 2013. |
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Lin, Dan-Yu, Donglin Zeng, and Zheng-Zheng Tang. SCORE-SeqTDS: Score tests for sequencing studies with trait-dependent sampling (C).. 3.0 ed., 2013. |
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Yi, Chanhee, Alexander Sibley, and Kouros Owzar. snplist: Tools to create gene sets (R).. 0.12 ed., 2013. |
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Hu, Yi-Juan, Dan-Yu Lin, Wei Sun, and Donglin Zeng. CNVstat: Statistical association analysis of copy number variants (C).. 1.0 ed., 2012. |
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Pang, Herbert. geneSelRSF: Gene selection using iterative recursive feature elimination (R).. 1.0 ed., 2012. |
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Walter, Vonn, Andrew B. Nobel, and Fred A. Wright. DiNAMIC: Discovering copy number aberrations manifested in cancer (R).., 2011. |
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He, Qianchuan, and Dan-Yu Lin. GWASelect: A variable selection method for genomewide association studies (C++).., 2011. |
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Shterev, Ivo D., Sin-Ho Jung, Stephen L. George, and Kouros Owzar. permGPU: Using graphics processing units in RNA microarray association studies (CUDA).., 2011. |
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Hu, Yi-Juan, Dan-Yu Lin, and Donglin Zeng. SNPMStat v4.0 : Statistical analysis of SNP-disease association with missing genotype data.., 2011. |
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Mitha, Faheem, Herodotos Herodotou, Nedyalko Borisov, Chen Jiang, Josh Yoder, and Kouros Owzar. SNPpy: Database management for SNP data from genome wide association studies.., 2011. |
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Hu, Yi-Juan, and Dan-Yu Lin. tagIMPUTE: Tag-based imputation.. 1.0 ed., 2010. |
