Research software

R packages

1. Asenso T, Zucknick M, Leoncio W, Zhang C (2025). MADMMplasso: Multi Variate Multi Response 'ADMM' with Interaction Effects. https://doi.org/10.32614/CRAN.package.MADMMplasso

2. Holst R, Leoncio W (2025). TruncExpFam: Truncated Exponential Family https://CRAN.R-project.org/package=TruncExpFam.

3. Matta T, Rutkowski L, Rutkowski D, Liaw Y, Leoncio W (2025). lsasim: Functions to Facilitate the Simulation of Large Scale Assessment Data. https://doi.org/10.32614/CRAN.package.lsasim.

4. Moreira-Soares Maurício (2025). BD4Predict: quality of life prediction tool for head and neck cancer survivors. https://ocbe-uio.github.io/bd4predict.
5. Romero-Becerra R (2025). SynergyLMM: Statistical Framework for in Vivo Drug Combination Studies. https://CRAN.R-project.org/package=SynergyLMM.
6. Zhao Z (2025). GPTCM: Generalized Promotion Time Cure Model with Bayesian Shrinkage Priors. https://github.com/ocbe-uio/GPTCM.
7. Banterle M, Zhao Z, Lewin A, Zucknick M (2025). BayesSUR: Bayesian Seemingly Unrelated Regression Models in High-Dimensional Settings. https://doi.org/10.32614/CRAN.package.BayesSUR.
8. Fagerland M (2024). contingencytables: Statistical Analysis of Contingency Tables. https://CRAN.R-project.org/package=contingencytables.
9. Hubin A, Leoncio W (2024). EMJMCMC: Evolutionary Mode Jumping Markov Chain Monte Carlo Expert Toolbox. https://CRAN.R-project.org/package=EMJMCMC.

10. Leoncio W, Ruxton G, Fagerland M (2024). permChacko: Chacko Test for Order-Restriction with Permutation. https://CRAN.R-project.org/package=permChacko.

11. Plaksienko A, Di Lena P, Nardini C, Angelini C (2024). methyLImp2: fast missing value estimation for DNA methylation data. https://www.bioconductor.org/packages/release/bioc/html/methyLImp2.html.

12. Zhao Z, Leoncio W, Madjar K, Østmo Hermansen T (2024). BayesSurvive: Bayesian Survival Models for High-Dimensional Data. https://doi.org/10.32614/CRAN.package.BayesSurvive.

13. Zhao Z, Zobolas J, Zucknick M, Aittokallio T (2024). survomics: Tutorial on survival modeling with applications to omics data. Bioinformatics https://10.1093/bioinformatics/btae132.

14. Zhao Z, Zucknick M, Saadati M, Benner A (2024). psbcSpeedUp: Penalized Semiparametric Bayesian Cox Models.https://doi.org/10.32614/CRAN.package.psbcSpeedUp.

15. Dietrich J, Leoncio W (2023). citation: Software Citation Tools. https://doi.org/10.32614/CRAN.package.citation

16. Ghannoum S, Köhn-Luque A, Leoncio W (2023). DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics. https://CRAN.R-project.org/package=DIscBIO.
17. Leoncio W (2023). matlab2r: Translation Layer from MATLAB to R. https://CRAN.R-project.org/package=matlab2r.

18. Ryalen P (2023). transform.hazards: Transforms Cumulative Hazards to Parameter Specified by ODE System. https://doi.org/10.32614/CRAN.package.transform.hazards.

19. Rønneberg L, Cremaschi A, Hanes R, Zhang C, Zucknick M (2023). bayesynergy: Bayesian semi-parametric modelling for in-vitro drug combination experiments. https://github.com/ocbe-uio/bayesynergy.

20. Vitelli V (2023). SparseFunClust: Sparse Functional Clustering. https://doi.org/10.32614/CRAN.package.SparseFunClust.

21. Ryalen P (2022). ahw: Calculates Continuous Time Likelihood Ratio Weights Assuming Multiplicative Intensity Models and Additive Hazard Models. https://doi.org/10.32614/CRAN.package.ahw.

22. Zhao Z, Zucknick M, Aittokallio T (2022). EnrichIntersect: an R package for custom set enrichment analysis and interactive visualization of intersecting sets. https://10.1093/bioadv/vbac073.

23. Ghannoum S, Fantini D, Leoncio W, Sørensen Ø (2021). cellmigRation: Track Cells, Analyze Cell Trajectories and Compute Migration Statistics. https://github.com/ocbe-uio/cellmigRation.

24. Thomas O, Leoncio W, Pesonen H, Corander J (2021). PriorElicitation: A Shiny app for prior elicitation. https://github.com/ocbe-uio/PriorElicitation.

25. Sørensen Ø, Crispino M, Liu Q, Vitelli V (2020). BayesMallows: An R Package for the Bayesian Mallows Model. https://doi.org/10.32614/RJ-2020-026.

26. Cremaschi A, Rønneberg L, Zucknick M (2019). synergysplines: Bayesian semi-parametric modelling for in-vitro drug combination experiments. https://github.com/ocbe-uio/synergysplines.

27. Zhao Z, Zucknick M (2019). IPFStructPenalty: Structured multiresponse penalized regression. https://github.com/zhizuio/IPFStructPenalty.

Python packages

1. Köhn-Luque A, Myklebust E M, Tadele D S, Giliberto M, Schmiester L, Noory J, ..., Foo J (2023). pyPhenoPop: Phenotypic deconvolution in heterogeneous cancer cell populations using drug-screening data. https://doi.org/10.1016/j.crmeth.2023.100417
2. Moreira-Soares M, Mossmann E, Travasso R D M, Bordin J R, TrajPy: empowering feature engineering for trajectory analysis across domains. Bioinformatics Advances, Volume 4, Issue 1, 2024, vbae026, https://doi:10.1093/bioadv/vbae026.
3. Lintusaari J, Vuollekoski H, Kangasrääsiö A, Skytén K, Järvenpää M, Marttinen P, Gutmann M U, Vehtari A, Corander J, Kaski S (2018). ELFI: Engine for Likelihood-Free Inference. http://jmlr.org/papers/v19/17-374.html

MATLAB packages

1. Myklebust E M, Köhn-Luque A, Arsenteva P (2022). PhenoPop: Phenotypic deconvolution in heterogeneous cancer cell populations using drug screen data. https://doi.org/10.5281/zenodo.7334379
2. Kamil A, Ghannoum S (2020). CellMAPtracer: A user-friendly tracking tool for long-term migratory and proliferating cells. https://doi.org/10.5281/zenodo.4319619
3. Corander J, Marttinen P, Siren J, Tang J, Cheng L (2012). BAPS: Bayesian Analysis of Population Structure. https://github.com/ocbe-uio/BAPS 

Final notes

• Software are listed in descending order of date, then alphabetically by surnames.
• The list is manually compiled from this source as well as internal records, and excludes software specifically meant for a teaching course or research project.
• For changes, please get in contact by e-mail.