Software

This website contains links to codes developed by Dr. Chekouo, together with some of the datasets used in their publications.

  • BIPnet R package implements an MCMC algorithm for a Bayesian analysis that integrates multi-omics data types, clinical covariates and clinical response variables

Reference paper: Thierry Chekouo and Sandra (2021), Bayesian Integrative Analysis and Prediction with Application to Atherosclerosis Cardiovascular Disease}, Biostatistics, In press.

  • BayesF2D R package for the implementation of an MCMC algorithm for a Bayesian Analysis for functional 2D data and performs prediction of a scalar response.

Reference paper: Thierry Chekouo, Shariq Mohammed and Arvind Rao (2020), A Bayesian 2D functional linear model for gray-level co-occurrence matrices in texture analysis of lower grade gliomas, NeuroImage: Clinical, Volume 28, Article 102437 [pdf]

  • BACkPAy R package for identifying patterns with (non) differential expression data using BACkPAy (BAyesian mixture model that efficiently determines Clusters of proteins with similar "pre-defined" expression PAtterns)

  • Pattern visualization (ShinyApp) for showing patterns for expression data obtained from BACkPAy. Data example, Manual.

  • Pattern visualization (ShinyApp) obtained from BACkPAy for the observed cell line proteomic data

Reference Paper: Thierry Chekouo et al (2020), Investigating protein patterns in human leukemia cell line experiments: A Bayesian approach for extremely small sample sizes, Statistical methods in medical research, Volume 29, Number 4, pages 1181-1196 [pdf]

  • Matlab Code for integrative Bayesian models for mRNAs and microRNAs.

Reference paper: Chekouo et al (2015). A Bayesian Integrative Approach to Biomarker Selection with Application to Kidney Cancer, Biometrics, Vol. 71, Issue 2, pages 428-438

  • Matlab Code for integrative Bayesian models for imaging genetics.

Reference paper: Thierry Chekouo et al (2016), A Bayesian predictive model for imaging genetics with application to schizophrenia, The Annals of Applied Statistics, Volume 10, Number 3 (2016), 1547-1571.

  • C code for integrative Bayesian approaches with unbalanced sample sizes

Reference paper: Thierry Chekouo et al (2017), A Bayesian integrative approach for multi-platform genomics data: a kidney cancer case study, Biometrics, Vol. 73, Issue 2, pages 615-623

  • Java code for the Penalized Biclustering model

Reference paper: Thierry Chekouo and Alejandro Murua (2015), The Penalized Biclustering model and Related Algorithms, Journal of Applied Statistics, vol. 42, issue 6, pages 1255-1277