| DOVE: Durability of Vaccine Efficacy |
|
https://dlin.web.unc.edu/software/dove/ |
|
| dtrSurv: Dynamic Treatment Regimes for Survival Analysis (R) |
Project 2.4 |
R package |
|
| CONCUR: Kernel-based association test for copy number variation (CNV) aggregate analysis (R) |
Project 2.3 |
CONCUR |
|
| ICODS: Data Analysis for ODS and Case-Cohort Designs with Interval-Censoring (R) |
Project 2.1 |
R Package on CRAN |
|
| CRM2DIM: Dual-Agent Bayesian Continual Reassessment Method (SAS) |
Project 2.1 |
Available from github |
|
| BTAD : Biomarker Threshold Adaptive Designs for Survival Endpoints (C++) |
Project 2.1 |
Software Implementation |
|
| AEBSD: Sample size of AEBSD and Comparison with BSD (R) |
Project 2.1 |
Available from github |
|
| BayesCTDesign: Two Arm Bayesian Clinical Trial Design with and Without Historical Control Data (R) |
Project 2.2 |
R Package on CRAN |
|
| Biomarker threshold adaptive designs for survival endpoints. |
Project 2.1 |
Software Implementation |
|
| apeglm: Approximate posterior estimation for GLM coefficients (R) |
Project 2.3 |
Available from Bioconductor |
|
| MultiTDS: Analysis of Sequence Data Under Multivariate Trait-Dependent Sampling (C++) |
Project 2.3 |
Software Implementation |
|
| CLOSE: A toolkit for CNA/LOH analysis with Sequencing data |
Project 2.3 |
Available from github |
|
| ASGENSENG: Detect Allele Specific CNV from Both WGS and WES Data (Python/Shell) |
Project 2.3 |
Available from sourceforge |
|
| MARATHON: Integrates Multiple Related Statistical Software for Copy Number Profiling and Downstream Analyses (R) |
Project 2.3 |
Available from github |
|
| TwoPhaseReg: Regression Analysis Under General Two-Phase Sampling (R) |
Project 2.3 |
Available from github |
|
| PreMeta: Facilitates the Exchange of Information Between Software Packages for Meta-Analysis (C++) |
Project 2.3 |
Available here |
|
| SynthEx: Tools for CNA detection and tumor heterogeneity profiling (R) |
Project 2.3 |
Available from github |
|
| DTRlearn: Learning Algorithms for Dynamic Treatment Regimes (R) |
Project 2.4 |
R package |
|
| sigclust2: Statistical Significance for Hierarchical Clustering (R) |
Project 2.3 |
Available from github |
|
| ADNI_RMRSS: Regression Models on Riemannian Symmetric Spaces (MATLAB) |
Project 2.2 |
Download Here |
|
| SUGEN: Genetic Association Analysis Under Complex Survey Sampling (C++) |
Project 2.3 |
Download From |
|
| SAME: Somatic mutation Association test with Measurement Errors (R) |
Project 2.3 |
R package |
|
| Galax (C++) |
Project 2.2 |
Available from Paul O. Lewis Laboratory Software |
|
| xmeta: A Toolbox for Multivariate Meta-Analysis (R) |
Project 2.2 |
R Package on CRAN |
|
| CODEX2: Full-spectrum copy number variation detection by high-throughput DNA sequencing. (R) |
Project 2.3 |
R package |
|
| POINT: Protein Structure Guided Local Test (R) |
Project 2.3 |
R Package on CRAN |
|
| Allele-specific copy-number discovery from whole-genome and whole-exome sequencing. |
Project 2.3 |
Software Implementation |
|
| Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny. |
Project 2.3 |
R package |
|
| Augmented outcome-weighted learning for estimating optimal dynamic treatment regimens. |
Project 2.4 |
R Package on CRAN |
|
| Efficient Semiparametric Inference Under Two-Phase Sampling, With Applications to Genetic Association Studies. |
Project 1.4, Project 2.3 |
R package |
|
| intcensROC: Fast Spline Function Based Constrained Maximum Likelihood Estimator for AUC Estimation of Interval Censored Survival Data (R) |
Project 1.4, Project 2.3 |
R Package on CRAN |
|
| groupedSurv: Efficient Estimation of Grouped Survival Models Using the Exact Likelihood Function (R) |
Project 1.4, Project 2.3 |
CRAN distribution |
|
| Semiparametric estimation of the accelerated failure time model with partly interval-censored data. |
Project 1.4, Project 2.3 |
R package |
|
| ICGOR: Fit Generalized Odds Rate Hazards Model with Interval Censored Data (R) |
Project 1.1, Project 2.1 |
R Package on CRAN |
|
| bcSeq: Fast Sequence Alignment for High-Throughput shRNA and CRISPR Screens (R) |
Project 2.3 |
Available from Bioconductor |
|
| GORCure: Fit Generalized Odds Rate Mixture Cure Model with Interval Censored Data (R) |
Project 2.1 |
R Package on CRAN |
|
| Simon’s like design with relaxed futility stopping (Web) |
Project 2.1 |
Web Implementation |
|
| fastJT: Efficient Jonckheere-Terpstra Test Statistics for Robust Machine Learning and Genome-Wide Association Studies (R) |
|
FastJT |
|
| CTD Systems (Java) |
Project 2.1 |
jar File, Read Me File |
|
| CTD Systems (Java) |
Project 2.1 |
jar File, Read Me File |
|
| PreMeta: a tool to facilitate meta-analysis of rare-variant associations. |
Project 1.4, Project 2.3 |
Software Implementation |
|
| SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling. |
Project 1.4, Project 2.3 |
R package |
|
| IntCens: Nonparametric maximum likelihood estimation for a broad class of semiparametric regression models with general interval-censored data (R). |
Project 2.3 |
R Package |
|
| AFNC: Adaptive false negative control (R) |
Project 2.3 |
R package |
|
| JAGUAR: Joint analysis of genotype and group-specific variability using a novel score test approach to map expression quantitative trait loci (eQTL) (R) |
Project 2.3 |
R Package |
|
| lclGWAS: Efficient estimation of discrete-time multivariate frailty model using exact likelihood function for grouped survival data (R). |
|
R package |
|
| NormalMean_BSS: Calculates the Bayesian sample size based on ACC, ALC, and WOC for normal model (SAS). |
Project 2.2 |
NormalMean_BSS |
|
| BPower: Computes two versions of Bayesian power for normal models (SAS). |
Project 2.2 |
bpower macro |
|
| jtGWAS: Efficient Jonckheere-Terpstra test statistics (R). |
|
R Package |
Vignette |
| subdetect: Detect subgroup with an enhanced treatment effect (R). |
Project 1.5, Project 2.4 |
R Package distributed by CRAN |
|
| Analysis of Sequence Data Under Multivariate Trait-Dependent Sampling. |
Project 2.3 |
Software Implementation |
|
| Global copy number profiling of cancer genomes. |
Project 2.3 |
Software Implementation |
|
| GGMridge: Gaussian graphical models using ridge penalty followed by thresholding and reestimation (R). |
Project 1.3 |
R Package distributed by CRAN |
|
| GHREG: Semiparametric general hazards rate model for right-censored data (C). |
Project 1.4, Project 2.1, Project 2.2 |
Software Distribution Page |
|
| SAS Macro BSMED: Bayesian survival meta-experimental design using historical data. |
Project 2.1 |
BSMED macro |
|
| RAMSVM: Reinforced angle-based multicategory support vector machines (R). |
Project 1.5, Project 2.3, Project 2.4 |
R package available on CRAN |
|
| RLT: Reinforcement learning trees (R). |
Project 1.5, Project 2.4 |
Distribution URL |
|
| SEQGWAS: Integrative analysis of sequencing and GWAS data (C/C++). |
Project 2.3 |
Download Site |
|
| skda: Sparse (multicategory) kernel discriminant analysis (R). |
Project 1.5 |
R Package |
|
| TRECASE_MLE: eQTL mapping based on total read count and allele-specific expression in RNA-Seq data with maximum-likelihood estimation (C/C++). |
Project 1.4 |
Zip Distribution |
|
| TensorGxG: A sparse and low-rank screening based on the combination of a low-rank interaction model and the Lasso screening (Matlab). |
Project 1.4 |
Matlab Implementation |
|
| BSMED: Bayesian survival meta-experimental design using historical data (SAS). |
Project 2.2 |
SAS Macro, Example |
|
| BSMED: Bayesian survival meta-experimental design using historical data (SAS). |
Project 2.2 |
SAS Macro, Example |
|
| Detection of gene-gene interactions using multistage sparse and low-rank regression. |
Project 2.3 |
Alternating Rank-1 Algorithm (matlab code) |
|
| modelObj: A model object framework for regression analysis (R). |
|
R Package |
|
| SurvLong: Analysis of proportional hazards model with sparse longitudinal covariates (R). |
Project 2.1, Project 2.3 |
R Package |
|
| AsynchLong: Regression analysis of sparse asynchronous longitudinal data (R). |
Project 2.1, Project 2.2 |
R Package |
|
| pcnetmeta: Methods for patient-centered network meta-analysis (R). |
Project 1.3 |
R Package |
|
| Joint Models of Longitudinal Data and Recurrent Events with Informative Terminal Event. |
Project 1.2, Project 2.1 |
R functions for method |
|
| JMDesign: Statistical design for joint models of longitudinal and survival data (R). |
Project 2.1 |
R Package |
|
| highTtest: Simultaneous critical values for t-tests in very high dimensions (R). |
Project 2.3 |
R Package (CRAN) |
|
| SNP_NLMM: Implement a flexible random effects density for generalized linear and nonlinear mixed models (SAS). |
Project 1.2 |
Software Download |
|
| SNPpy: Database management for SNP data from genome wide association studies. |
Project 2.3 |
Software Information, Downloads |
|
| SNPpy: Database management for SNP data from genome wide association studies. |
Project 2.3 |
Software Information, Downloads |
|
| Power calculations and confidence intervals in phase II design with over enrollment (SAS/R). |
Project 1.3 |
Software Download - SAS Macro for Confidence Intervals, Software Download - R functions for Power Calculations |
|
| Power calculations and confidence intervals in phase II design with over enrollment (SAS/R). |
Project 1.3 |
Software Download - SAS Macro for Confidence Intervals, Software Download - R functions for Power Calculations |
|
| Macros for missing data (SAS). |
Project 1.3 |
cox.ignore.macro, coxnonig.sasmacro , emexp.mac , emlog_sat.mac , emlogit.mac, empwexp.mac , empwexp_sat.mac |
Introduction Document |
| Macros for missing data (SAS). |
Project 1.3 |
cox.ignore.macro, coxnonig.sasmacro , emexp.mac , emlog_sat.mac , emlogit.mac, empwexp.mac , empwexp_sat.mac |
Introduction Document |
| Macros for missing data (SAS). |
Project 1.3 |
cox.ignore.macro, coxnonig.sasmacro , emexp.mac , emlog_sat.mac , emlogit.mac, empwexp.mac , empwexp_sat.mac |
Introduction Document |
| Macros for missing data (SAS). |
Project 1.3 |
cox.ignore.macro, coxnonig.sasmacro , emexp.mac , emlog_sat.mac , emlogit.mac, empwexp.mac , empwexp_sat.mac |
Introduction Document |
| Macros for missing data (SAS). |
Project 1.3 |
cox.ignore.macro, coxnonig.sasmacro , emexp.mac , emlog_sat.mac , emlogit.mac, empwexp.mac , empwexp_sat.mac |
Introduction Document |
| Macros for missing data (SAS). |
Project 1.3 |
cox.ignore.macro, coxnonig.sasmacro , emexp.mac , emlog_sat.mac , emlogit.mac, empwexp.mac , empwexp_sat.mac |
Introduction Document |
| Macros for missing data (SAS). |
Project 1.3 |
cox.ignore.macro, coxnonig.sasmacro , emexp.mac , emlog_sat.mac , emlogit.mac, empwexp.mac , empwexp_sat.mac |
Introduction Document |
| Perturbation and scaled Cook's distance (C++/Matlab). |
Project 1.3 |
Software Download, Supplement Document |
|
| Perturbation and scaled Cook's distance (C++/Matlab). |
Project 1.3 |
Software Download, Supplement Document |
|
| Bayesian Lasso for semiparametric structural equation models toolkit (C++). |
Project 1.3 |
Software Download |
|
| Fixed and random effects selection in mixed effects toolkit (R). |
Project 1.3 |
Software Download |
|
| CR: Power calculation for weighted log-rank tests in cure rate models (R). |
Project 1.3 |
R Package (cran) |
|
| Fixed: Bayesian meta-experimental design (SAS). |
Project 1.3 |
SAS macro |
|
| RSNPset: Genome-wide SNP set analysis on the basis of efficient scores (R). |
Project 2.3 |
R package |
Vignette (tutorial) |
| Sample size determination in shared frailty models for multivariate time-to-event data. |
Project 2.1 |
R package |
|
| mmeta: Multivariate meta-analysis (R). |
Project 2.1 |
R Package available from Cran |
|
| Fixed and random effects selection in mixed effects models. |
Project 1.3 |
Fixed and Random Effects Selection in Mixed Effects Toolkit |
|
| snplist: Tools to create gene sets (R). |
Project 2.3 |
R Package |
Tutorial |
| geneSelRSF: Gene selection using iterative recursive feature elimination (R). |
Project 2.1, Project 2.3 |
geneSelRSF Home Page |
|
| tagIMPUTE: Tag-based imputation. |
Project 2.3 |
tagIMPUTE Home Page |
|
| MOST: Multivariate outcome score test (C). |
Project 2.3 |
MOST Home Page |
|
| MASS: Meta-analysis of sequencing studies (C). |
Project 2.3 |
MASS Home Page |
|
| SCORE-SeqTDS: Score tests for sequencing studies with trait-dependent sampling (C). |
Project 2.3 |
SCORE-SeqTDS Home Page |
|
| SCORE-Seq: Score tests for detecting disease associations with rare variants in sequencing studies (C). |
Project 2.3 |
SCORE-Seq Home Page |
|
| CNVstat: Statistical association analysis of copy number variants (C). |
Project 2.3 |
CNVstat Home Page |
|
| iqLearn: Interactive Q-learning (R). |
Project 2.4 |
Package Download |
|
| SNPMStat v4.0 : Statistical analysis of SNP-disease association with missing genotype data. |
Project 2.3 |
Software Homepage |
|
| survSNP: Power and sample size calculations for SNP association studies with censored time-to-event outcomes (R). |
Project 2.1 |
Software Distribution, Software Development |
|
| survSNP: Power and sample size calculations for SNP association studies with censored time-to-event outcomes (R). |
Project 2.1 |
Software Distribution, Software Development |
|
| Power and sample size calculation for microarray studies (Fortran). |
Project 2.1 |
Source Code - Fortran |
|
| permGPU: Using graphics processing units in RNA microarray association studies (CUDA). |
Project 2.3 |
Software Information, Download permGPU and Tutorials |
|
| permGPU: Using graphics processing units in RNA microarray association studies (CUDA). |
Project 2.3 |
Software Information, Download permGPU and Tutorials |
|
| Sample size calculation for comparing survival curves under general hypotheses testing (Fortran). |
Project 2.1 |
Fortran Code |
|
| odsroc: Nonparametric estimation of AUC and partial AUC under test-result-dependent sampling (R). |
Project 2.1 |
Software Information, Software Distribution |
|
| odsroc: Nonparametric estimation of AUC and partial AUC under test-result-dependent sampling (R). |
Project 2.1 |
Software Information, Software Distribution |
|
| HSSVD: Biclustering with heterogeneous variance (R). |
Project 2.3 |
Package available on CRAN |
|
| GWASelect: A variable selection method for genomewide association studies (C++). |
Project 2.3 |
Software Information, Download GWQSelect, WTCCC data |
|
| GWASelect: A variable selection method for genomewide association studies (C++). |
Project 2.3 |
Software Information, Download GWQSelect, WTCCC data |
|
| GWASelect: A variable selection method for genomewide association studies (C++). |
Project 2.3 |
Software Information, Download GWQSelect, WTCCC data |
|
| DiNAMIC: Discovering copy number aberrations manifested in cancer (R). |
Project 2.3 |
Overview PDF, DiNAMIC code, Sample code and data files |
|
| DiNAMIC: Discovering copy number aberrations manifested in cancer (R). |
Project 2.3 |
Overview PDF, DiNAMIC code, Sample code and data files |
|
| DiNAMIC: Discovering copy number aberrations manifested in cancer (R). |
Project 2.3 |
Overview PDF, DiNAMIC code, Sample code and data files |
|
| logi: Logistic regression using forward selection (R). |
|
Software Package (ZIP), Software Package (TAR.gz) |
|
| logi: Logistic regression using forward selection (R). |
|
Software Package (ZIP), Software Package (TAR.gz) |
|
| Haplo.CasGLM: Haplotype specific simultaneous factor selection and collapsing levels in GLM (R). |
Project 1.2, Project 2.3, Project 2.4 |
Software Package (ZIP), Software Package (TAR.gz) |
|
| Haplo.CasGLM: Haplotype specific simultaneous factor selection and collapsing levels in GLM (R). |
Project 1.2, Project 2.3, Project 2.4 |
Software Package (ZIP), Software Package (TAR.gz) |
|
| doublyRobust: Doubly robust estimation for monotonely coarsened data in longitudinal studies with dropout and/or incomplete data (R). |
Project 1.2 |
Software Package (TAR.gz) |
|
| CasANOVA: Simultaneous factor selection and collapsing levels in ANOVA (R). |
Project 1.2, Project 2.3, Project 2.4 |
Software Package (ZIP) , Software Package (TAR.gz) |
|
| CasANOVA: Simultaneous factor selection and collapsing levels in ANOVA (R). |
Project 1.2, Project 2.3, Project 2.4 |
Software Package (ZIP) , Software Package (TAR.gz) |
|
| Variable selection for optimal treatment decision. |
Project 2.1, Project 2.3, Project 2.4 |
R Package |
|
| Bayesian meta-experimental design: evaluating cardiovascular risk in new antidiabetic therapies to treat type 2 diabetes. |
Project 1.3 |
Fixed: SAS macro for carrying out Bayesian meta-experimental design |
|
