Clinical tools, R packages, and legacy utilities are grouped below with links to papers and code.
Decision Support Tools & Patents
PurIST Pancreatic Classifier
Single-sample PDAC subtype assay used in cooperative trials.
- Patents:
- US 11,053,550 (July 2021) – Gene-expression based subtyping of PDAC
- US Patent App. 17/336,600 (April 2022) – Methods and compositions for prognostic/diagnostic subtyping
- US 12,000,003 (June 2024) – Platform-independent single sample classifier
- Key papers: Rashid et al., Clin Cancer Res (2020); Li et al., J Mol Diagnostics (2024)
- Code: GitHub · Shiny GUI
R Packages
BATON
Bayesian adaptive trial operating-characteristic tuning for platform trials.
- GitHub
- In development (2025)
evolveTrial
Adaptive monitoring and simulation tools for evolutionary clinical trial designs.
- GitHub
- In development (2025)
deSurv
De-biased survival estimators pairing flexible ML bases with biomarker-rich trial data.
- GitHub
- In development (2025)
dlglm
Deeply learned GLMs handling non-ignorable missingness.
- GitHub
- Lim et al., JCGS (2024)
NIMIWAE
Variational autoencoder for non-ignorable missing data.
- GitHub
- Lim et al., Stat Biopharm Res (2024)
glmmPen
Penalized GLMM selection for biomarker discovery.
CompDTUReg
Differential transcript usage with quantification uncertainty.
- GitHub
- Young et al., Biostatistics (2023)
epigraHMM
Multi-sample enrichment detection for ChIP/ATAC.
- Bioconductor · GitHub
- Baldoni et al., Biometrics (2022)
FSCseq
Model-based feature selection + clustering for RNA-seq.
- GitHub
- Lim et al., Ann Appl Stat (2021)
Legacy & Specialized Tools
- mixNBHMM – Differential peak calling for multi-condition epigenomic data. (GitHub)
- ZIMHMM – Consensus enrichment calling across ChIP-seq replicates. (GitHub)
- ZINBA – Zero-inflated negative binomial algorithm detecting NGS-enriched regions. (Archived; formerly hosted on Google Code)
- hmmcov – HMM / AR-HMM procedures with variable selection for epigenetic enrichment. (Archived; formerly hosted on Google Code)
- BASeG – Bivariate association studies linking expression and epigenetic marks with shared genetics. (Rashid et al., Ann Appl Stat, 2016)
Code Repositories
All software is actively maintained on GitHub. Contributions, issues, and feature requests are welcome, and the full repository + contributor stats live on the Repositories page.
Collaborative Development
Many packages are developed in close collaboration with lab members and trainees:
- Hillary Heiling: glmmPen lead developer
- David Lim: dlglm, NIMIWAE, FSCseq lead developer
- Pedro Baldoni: epigraHMM, mixNBHMM, ZIMHMM lead developer
- Scott Van Buren: CompDTUReg lead developer
- Amber Young: CompDTUReg co-developer; current PhD student working on semi-supervised matrix factorization for PDAC subtyping
Support & Contact
For technical support, please open an issue on the relevant GitHub repository. For collaboration inquiries, contact naim@unc.edu.