Overview

Software & Tooling

Open-source software packages and tools for statistical genomics and cancer research

Clinical tools, R packages, and legacy utilities are grouped below so collaborators can jump straight to validated builds.

  • PurIST CLIA assay + TrialMatch navigation stack
  • Bioconductor / CRAN releases for GLMMs, DTU, and imputation
  • Legacy research utilities archived with documentation

Clinical Tools & Patents

PurIST Pancreatic Classifier

CLIA-ready, single-sample PDAC subtype assay embedded in cooperative trials.

  • Patent: US 12,000,003 (June 2024)
  • Key paper: Rashid et al., Clin Cancer Res (2020)
  • Code: GitHub · Shiny GUI

R Packages

glmmPen

Penalized GLMM selection for biomarker discovery.

  • CRAN · GitHub
  • Heiling et al., The R Journal (2024)

epigraHMM

Multi-sample enrichment detection for ChIP/ATAC.

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)

FSCseq

Model-based feature selection + clustering for RNA-seq.

  • GitHub
  • Lim et al., Ann Appl Stat (2021)

CompDTUReg

Differential transcript usage with quantification uncertainty.

  • GitHub
  • Young et al., Biostatistics (2023)

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. (Project)
  • hmmcov – HMM / AR-HMM procedures with variable selection for epigenetic enrichment. (Project)
  • 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.