Software - All

DOVE: Durability of Vaccine Efficacy, Line, D., Zeng, D., Holloway, S.T., (2021)
CONCUR: Kernel-based association test for copy number variation (CNV) aggregate analysis (R), Brucker, A., Holloway, S.T., Tzeng, J.Y., (2020)
dtrSurv: Dynamic Treatment Regimes for Survival Analysis (R), Holloway, S., Cho, H., (2020)
CRM2DIM: Dual-Agent Bayesian Continual Reassessment Method (SAS), Bayar, M., Ivanova, A., Le Teuff, G., (2019)
ICODS: Data Analysis for ODS and Case-Cohort Designs with Interval-Censoring (R), Holloway, S.T., Zhou, Q., Cai, J., Zhou, H., (2019)
POINT: Protein Structure Guided Local Test (R), West, R.Marceau, Holloway, S.T., (2019)
AEBSD: Sample size of AEBSD and Comparison with BSD (R), Wang, T., (2018)
apeglm: Approximate posterior estimation for GLM coefficients (R), Zhu, A., Ibrahim, J.G., Love, M.I., (2018)
BayesCTDesign: Two Arm Bayesian Clinical Trial Design with and Without Historical Control Data (R), Eggleston, B.S., Wilson, D., McNeil, B., Ibrahim, J.G., Catellier, D., (2018)
BTAD : Biomarker Threshold Adaptive Designs for Survival Endpoints (C++), Diao, G., Dong, J., Zeng, D., Ibrahim, J.G., (2018)
CODEX2: Full-spectrum copy number variation detection by high-throughput DNA sequencing. (R), Jiang, Y., Zhang, N.R., (2018)
DTRlearn: Learning Algorithms for Dynamic Treatment Regimes (R), Liu, Y., Wang, Y., Zeng, D., (2018)
groupedSurv: Efficient Estimation of Grouped Survival Models Using the Exact Likelihood Function (R), Lin, J., Sibley, A., Truong, T., Owzar, K., Li, Z., (2018)
intcensROC: Fast Spline Function Based Constrained Maximum Likelihood Estimator for AUC Estimation of Interval Censored Survival Data (R), Lin, J., Wu, Y., Wang, X.F., Owzar, K., (2018)
MARATHON: Integrates Multiple Related Statistical Software for Copy Number Profiling and Downstream Analyses (R), Urrutia, E., Chen, H., Zhou, Z., Zhang, N.R., Jiang, Y., (2018)
SAME: Somatic mutation Association test with Measurement Errors (R), Liu, Y., Sun, W., He, Q., (2018)
TwoPhaseReg: Regression Analysis Under General Two-Phase Sampling (R), Tao, R., (2018)
BayesProp: Bayesian Clinical Trial Design for Regression Models Using Historical Data (SAS), Ibrahim, J.G., Psioda, M., (2017)
bcSeq: Fast Sequence Alignment for High-Throughput shRNA and CRISPR Screens (R), (2017)
CTD Systems (Java), Jung, S.H., (2017)
CureBayes: Bayesian phase 3 design using the cure rate model. (SAS and R), Ibrahim, J.G., Psioda, M., (2017)
DynTxRegime: A comprehensive package for analysis of dynamic treatment regimes (R)., Holloway, S.T., Laber, E.B., Linn, K.A., Zhang, B., Davidian, M., Tsiatis, A.A., (2017)
fastJT: Efficient Jonckheere-Terpstra Test Statistics for Robust Machine Learning and Genome-Wide Association Studies (R), Lin, J., Sibley, A., Shterev, I.D., Owzar, K., (2017)
GORCure: Fit Generalized Odds Rate Mixture Cure Model with Interval Censored Data (R), Zhou, J., Zhang, J., Lu, W., (2017)
ICGOR: Fit Generalized Odds Rate Hazards Model with Interval Censored Data (R), Zhou, J., Zhang, J., Lu, W., (2017)
PICAFT: Semiparametric Estimation of the Accelerated Failure Time Model With Partly Interval-Censored Data (R), Gao, F., Zeng, D., Lin, D.Y., (2017)
PreMeta: Facilitates the Exchange of Information Between Software Packages for Meta-Analysis (C++), Tang, Z.Z., Bunn, P., Tao, R., Liu, Z., Lin, D.Y., (2017)
Simon’s like design with relaxed futility stopping (Web), Ivanova, A., Deal, A., (2017)
SynthEx: Tools for CNA detection and tumor heterogeneity profiling (R), Chen, M., (2017)
xmeta: A Toolbox for Multivariate Meta-Analysis (R), Chen, Y., Hong, C., Chu, H., Liu, Y., (2017)
ADNI_RMRSS: Regression Models on Riemannian Symmetric Spaces (MATLAB), Cornea, E., Zhu, H., Kim, P., Ibrahim, J.G., (2016)
AFNC: Adaptive false negative control (R), Jeng, J., Daye, Z.John, Lu, W., Tzeng, J.Y., (2016)
AsynchLong: Regression analysis of sparse asynchronous longitudinal data (R)., Cao, H., Zeng, D., Fine, J.P., Holloway, S.T., (2016)
BetaBinPredProb: Compute predictive probabilities in Bayesian design for Phase IIA trials in a beta-binomial case (SAS)., Psioda, M., Ibrahim, J.G., (2016)
binDesign: Bayesian sample size for non-inferiority randomized trials with binary data (SAS)., Psioda, M., Ibrahim, J.G., (2016)
binDesignPP: Bayesian sample size for non-inferiority randomized trials with binary data with power prior (SAS)., Psioda, M., Ibrahim, J.G., (2016)
BPower: Computes two versions of Bayesian power for normal models (SAS)., Psioda, M., Ibrahim, J.G., (2016)
CLOSE: A toolkit for CNA/LOH analysis with Sequencing data, Wang, X., Chen, M., Yu, X., Pornputtapong, N., Chen, H., Zhang, N.R., Powers, S., Krauthammer, M., (2016)
design_biomAR: Bayes adaptive randomization for the probit model (SAS)., Psioda, M., Ibrahim, J.G., (2016)
fitRE: Bayesian superiority design for gamma frailty recurrent events model (SAS)., Psioda, M., Ibrahim, J.G., (2016)
Galax (C++), Lewis, P.O., (2016)
GGMridge: Gaussian graphical models using ridge penalty followed by thresholding and reestimation (R)., Ha, M.Jin, Holloway, S.T., (2016)
IntCens: Nonparametric maximum likelihood estimation for a broad class of semiparametric regression models with general interval-censored data (R)., Bunn, P., Zeng, D., Lin, D.Y., (2016)
JAGUAR: Joint analysis of genotype and group-specific variability using a novel score test approach to map expression quantitative trait loci (eQTL) (R), Acharya, C.R., McCarthy, J.M., Owzar, K., Allen, A.S., (2016)
jtGWAS: Efficient Jonckheere-Terpstra test statistics (R)., Lin, J., Sibley, A., Shterev, I.D., Owzar, K., (2016)
lclGWAS: Efficient estimation of discrete-time multivariate frailty model using exact likelihood function for grouped survival data (R)., Lin, J., Sibley, A., Truong, T., Cox, N., Dolan, E., Jiang, Y., McCarthy, J.M., Allen, A.S., Owzar, K., Li, Z., (2016)
MultiARMSBinary: Simulates Bayes adaptive randomization of multiple arms in a beta-binomial simulation (SAS)., Psioda, M., Ibrahim, J.G., (2016)
NormalMean_BSS: Calculates the Bayesian sample size based on ACC, ALC, and WOC for normal model (SAS)., Psioda, M., Ibrahim, J.G., (2016)
normDesign: Bayesian sample size for non-inferiority randomized trials with normal data (SAS)., Psioda, M., Ibrahim, J.G., (2016)
normDesignPP: Bayesian sample size for non-inferiority randomized trials with normal data with power prior (SAS)., Psioda, M., Ibrahim, J.G., (2016)
OTRselect: Variable selection for optimal treatment decision (R)., Lu, W., Zhang, H.Helen, Zeng, D., Geng, Y., Holloway, S.T., (2016)
RAMSVM: Reinforced angle-based multicategory support vector machines (R)., Zhang, C., Liu, Y., Holloway, S.T., (2016)
sigclust2: Statistical Significance for Hierarchical Clustering (R), Kimes, P., (2016)
subdetect: Detect subgroup with an enhanced treatment effect (R)., Fan, A., Holloway, S.T., (2016)
ASGENSENG: Detect Allele Specific CNV from Both WGS and WES Data (Python/Shell), Wang, W.B., Wang, W., Sun, W., Crowley, J.J., Szatkiewicz, J.P., (2015)
BSMED: Bayesian survival meta-experimental design using historical data (SAS)., Ibrahim, J.G., Gwon, Y., Chen, M.H., (2015)
FastKM: A fast multiple-kernel method based on a low-rank approximation (R)., Marceau, R., Lu, W., Sale, M.M., Worrall, B.B., Williams, S.R., Hsu, F.C., Tzeng, J.Y., Holloway, S.T., (2015)
fitDNM: Test of de novo enrichment that incorporates functional information (R)., Jiang, Y., Han, Y., Petrovski, S., Owzar, K., Goldstein, D.B., Allen, A.S., (2015)
modelObj: A model object framework for regression analysis (R)., Holloway, S.T., (2015)
MultiTDS: Analysis of Sequence Data Under Multivariate Trait-Dependent Sampling (C++), Tao, R., Zeng, D., Franceschini, N., North, K.E., Boerwinkle, E., Lin, D.Y., (2015)
RLT: Reinforcement learning trees (R)., Zhu, R., Kosorok, M.R., (2015)
SEQGWAS: Integrative analysis of sequencing and GWAS data (C/C++)., Hu, Y.J., Li, Y., Auer, P.L., Lin, D.Y., (2015)
SurvLong: Analysis of proportional hazards model with sparse longitudinal covariates (R)., Cao, H., Churpek, M.M., Zeng, D., Fine, J.P., Holloway, S.T., (2015)
TensorGxG: A sparse and low-rank screening based on the combination of a low-rank interaction model and the Lasso screening (Matlab)., Hung, H., Lin, Y.T., Chen, P., Wang, C.C., Huang, S.Y., Tzeng, J.Y., (2015)
TRECASE_MLE: eQTL mapping based on total read count and allele-specific expression in RNA-Seq data with maximum-likelihood estimation (C/C++)., Song, G., (2015)
cSFM: Covariate-adjusted skewed functional model (R)., Li, M., Staicu, A.M., Bondell, H.D., (2014)
highTtest: Simultaneous critical values for t-tests in very high dimensions (R)., Cao, H., Kosorok, M.R., Holloway, S.T., (2014)
JMfit - For fitting joint models for longitudinal and survival data (SAS), Zhang, D., Chen, M.H., Ibrahim, J.G., (2014)
Macros for missing data (SAS)., Ibrahim, J.G., Lipsitz, S., (2014)
mcc: Moment corrected correlation an approximation to exact association testing of two vectors (R)., Zhou, Y.H., (2014)
mmeta: Multivariate meta-analysis (R)., Luo, S., Chen, Y., Su, X., Chu, H., (2014)
pcnetmeta: Methods for patient-centered network meta-analysis (R)., Lin, L., Zhang, J., Chu, H., (2014)
Power calculations and confidence intervals in phase II design with over enrollment (SAS/R)., Gao, F., Zeng, D., Ibrahim, J.G., (2014)
RSNPset: Genome-wide SNP set analysis on the basis of efficient scores (R)., Yi, C., Sibley, A., Owzar, K., (2014)
SNP_NLMM: Implement a flexible random effects density for generalized linear and nonlinear mixed models (SAS)., Vock, D.M., Davidian, M., Tsiatis, A.A., (2014)
SUGEN: Genetic Association Analysis Under Complex Survey Sampling (C++), Lin, D.Y., Tao, R., Kalsbeek, W., Zeng, D., Gonzalez, F., Fernández-Rhodes, L., Graff, M., Koch, G.G., North, K.E., Heiss, G., (2014)
CasANOVA: Simultaneous factor selection and collapsing levels in ANOVA (R)., Bondell, H.D., Holloway, S.T., (2013)
doublyRobust: Doubly robust estimation for monotonely coarsened data in longitudinal studies with dropout and/or incomplete data (R)., Tsiatis, A.A., Davidian, M., Cao, W., Holloway, S.T., (2013)
GHREG: Semiparametric general hazards rate model for right-censored data (C)., Diao, G., (2013)
Haplo.CasGLM: Haplotype specific simultaneous factor selection and collapsing levels in GLM (R)., Bondell, H.D., Tzeng, J.Y., Koehler, M.L., Holloway, S.T., (2013)
HSSVD: Biclustering with heterogeneous variance (R)., Chen, G., Kosorok, M.R., (2013)
iqLearn: Interactive Q-learning (R)., Linn, K.A., Laber, E.B., Stefanski, L.A., (2013)
logi: Logistic regression using forward selection (R)., Boos, D.D., Holloway, S.T., (2013)
MASS: Meta-analysis of sequencing studies (C)., Tang, Z.Z., Lin, D.Y., (2013)
MOST: Multivariate outcome score test (C)., He, Q., Lin, D.Y., (2013)
SCORE-Seq: Score tests for detecting disease associations with rare variants in sequencing studies (C)., Lin, D.Y., Tang, Z.Z., (2013)
SCORE-SeqTDS: Score tests for sequencing studies with trait-dependent sampling (C)., Lin, D.Y., Zeng, D., Tang, Z.Z., (2013)
skda: Sparse (multicategory) kernel discriminant analysis (R)., Stefanski, L.A., Wu, Y., White, K., (2013)
snplist: Tools to create gene sets (R)., Yi, C., Sibley, A., Owzar, K., (2013)
CNVstat: Statistical association analysis of copy number variants (C)., Hu, Y.J., Lin, D.Y., Sun, W., Zeng, D., (2012)
CR: Power calculation for weighted log-rank tests in cure rate models (R)., Cornea, E., Qaqish, B., Ibrahim, J.G., (2012)
Fixed: Bayesian meta-experimental design (SAS)., Ibrahim, J.G., Chen, M.H., Xia, A., Liu, T., (2012)
geneSelRSF: Gene selection using iterative recursive feature elimination (R)., Pang, H., (2012)
JMDesign: Statistical design for joint models of longitudinal and survival data (R)., Cornea, E., Chen, L.M., Qaqish, B., Chu, H., Ibrahim, J.G., (2012)
odsroc: Nonparametric estimation of AUC and partial AUC under test-result-dependent sampling (R)., Wang, X., Ma, J., George, S.L., Zhou, H., (2012)
Perturbation and scaled Cook's distance (C++/Matlab)., Zhu, H., Ibrahim, J.G., Cho, H., (2012)
Power and sample size calculation for microarray studies (Fortran)., Jung, S.H., Young, S., (2012)
Sample size calculation for comparing survival curves under general hypotheses testing (Fortran)., Jung, S.H., Chow, S.C., (2012)
survSNP: Power and sample size calculations for SNP association studies with censored time-to-event outcomes (R)., Jung, S.H., Young, S., (2012)
Bayesian Lasso for semiparametric structural equation models toolkit (C++)., Guo, R., Zhu, H., Chow, S.M., Ibrahim, J.G., (2011)
DiNAMIC: Discovering copy number aberrations manifested in cancer (R)., Walter, V., Nobel, A.B., Wright, F.A., (2011)
Fixed and random effects selection in mixed effects toolkit (R)., Ibrahim, J.G., Zhu, H., Garcia, R.I., Guo, R., (2011)
GWASelect: A variable selection method for genomewide association studies (C++)., He, Q., Lin, D.Y., (2011)
permGPU: Using graphics processing units in RNA microarray association studies (CUDA)., Shterev, I.D., Jung, S.H., George, S.L., Owzar, K., (2011)
SNPMStat v4.0 : Statistical analysis of SNP-disease association with missing genotype data., Hu, Y.J., Lin, D.Y., Zeng, D., (2011)
SNPpy: Database management for SNP data from genome wide association studies., Mitha, F., Herodotou, H., Borisov, N., Jiang, C., Yoder, J., Owzar, K., (2011)
tagIMPUTE: Tag-based imputation., Hu, Y.J., Lin, D.Y., (2010)