A repo for some of my MDI helper functions.

R package for Bayesian mixture models and Multiple Dataset Integraiton, an extrapolation of mixture models to the multiple dataset context.

Semi-supervised and unsupervised Bayesian mixture models that simultaneously infer the cluster/class structure and a batch correction. Densities available are the multivariate normal and the multiv…

Paper specific scripts.

Personal website

Bayesian mixture models with accounting for batch effects.

Repository for the scripts to reproduce the results from the paper "A semi-supervised Bayesian mixture modelling approach for joint batch correction and classification".

Paper attempts

R package for consensus clustering of Bayesian mixture models.

Repo for work with Chris Wallace in Camridge.

Functions for plotting layout of umap object (from function umap::umap).

A container of things from my PhD that fit nowhere else better and are not important enough to form their own repo.

R package to extend TAGM to include multiple dataset integration.

Thesis MSc in Bioinformatics. Supervised by Chris Wallace and Bas Zwaan.

Notes and code for modelling the Farquhar-van Caemmerer-Berry model of steady-state photosynthesis.

The blogdown scripts generating the website at stcolema.github.io

Some tutorial for generic ML methods

Notes on extending Multiple Dataset Integration (MDI) to cover T-Augmented Gaussian Mixtured (TAGM) models.

Initial foray into semi-supervised / unsupervised learning using Bayesian mixture of models. The package uses C++ to do most of the heavy lifting.

Code for course BIF31306 in WUR. Code includes dna alignment code, kmeans clustering and hmm among others.

Code for WUR course Advanced Bioinformatics.

Case studies from WUR Modern Statistics for Life Sciences course

Code for my undergrad thesis analysing human eye movement across 2D and 3D video. It's my first proper foray into R and is quite horrible.