stcolema
I work with Bayesian methods for uncovering latent structure in biomedical assays. My main work to date has focused on clustering.
Pinned Repositories
batchmix
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 multivariate t. The model sampler is implemented in C++. This package is aimed at analysis of low-dimensional data generated across several batches. See [Coleman et al., 2022](https://doi.org/10.1101/2022.01.14.476352) for details of the model.
MDIr
R package for Bayesian mixture models and Multiple Dataset Integraiton, an extrapolation of mixture models to the multiple dataset context.
photosynthesis
Notes and code for modelling the Farquhar-van Caemmerer-Berry model of steady-state photosynthesis.
mdiHelpR
A repo for some of my MDI helper functions.
ABG30806-Modern_statistics_for_life_sciences
Case studies from WUR Modern Statistics for Life Sciences course
BatchClassifierPaper
Repository for the scripts to reproduce the results from the paper "A semi-supervised Bayesian mixture modelling approach for joint batch correction and classification".
BatchMixtureModel
Bayesian mixture models with accounting for batch effects.
BayesicGibbs
Initial foray into semi-supervised / unsupervised learning using Bayesian mixture of models. The package uses C++ to do most of the heavy lifting.
BIF30806_AdvBioinformatics
Code for WUR course Advanced Bioinformatics.
BIF31306_Algorithms_bioinformatics
Code for course BIF31306 in WUR. Code includes dna alignment code, kmeans clustering and hmm among others.
stcolema's Repositories
stcolema/mdiHelpR
A repo for some of my MDI helper functions.
stcolema/MDIr
R package for Bayesian mixture models and Multiple Dataset Integraiton, an extrapolation of mixture models to the multiple dataset context.
stcolema/batchmix
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 multivariate t. The model sampler is implemented in C++. This package is aimed at analysis of low-dimensional data generated across several batches. See [Coleman et al., 2022](https://doi.org/10.1101/2022.01.14.476352) for details of the model.
stcolema/tagmmdi_wd
Paper specific scripts.
stcolema/stcolema.github.io
Personal website
stcolema/tagmmdiReDraft
stcolema/BatchMixtureModel
Bayesian mixture models with accounting for batch effects.
stcolema/BatchClassifierPaper
Repository for the scripts to reproduce the results from the paper "A semi-supervised Bayesian mixture modelling approach for joint batch correction and classification".
stcolema/ConsensusClusteringForBayesianMixtureModels
Paper attempts
stcolema/ccbm
R package for consensus clustering of Bayesian mixture models.
stcolema/CarDEC_Codes
Fork of code to recreate analysis from [this paper](https://www.biorxiv.org/content/10.1101/2020.09.23.310003v1).
stcolema/ra_chris_wallace
Repo for work with Chris Wallace in Camridge.
stcolema/uplotter
Functions for plotting layout of umap object (from function umap::umap).
stcolema/PhD
A container of things from my PhD that fit nowhere else better and are not important enough to form their own repo.
stcolema/tagmmdi
R package to extend TAGM to include multiple dataset integration.
stcolema/WUR_genetics_thesis
Thesis MSc in Bioinformatics. Supervised by Chris Wallace and Bas Zwaan.
stcolema/photosynthesis
Notes and code for modelling the Farquhar-van Caemmerer-Berry model of steady-state photosynthesis.
stcolema/blogdown_github_pages
The blogdown scripts generating the website at stcolema.github.io
stcolema/ML_tutorials
Some tutorial for generic ML methods
stcolema/tagmmdi_notes
Notes on extending Multiple Dataset Integration (MDI) to cover T-Augmented Gaussian Mixtured (TAGM) models.
stcolema/BayesicGibbs
Initial foray into semi-supervised / unsupervised learning using Bayesian mixture of models. The package uses C++ to do most of the heavy lifting.
stcolema/BIF31306_Algorithms_bioinformatics
Code for course BIF31306 in WUR. Code includes dna alignment code, kmeans clustering and hmm among others.
stcolema/BIF30806_AdvBioinformatics
Code for WUR course Advanced Bioinformatics.
stcolema/ABG30806-Modern_statistics_for_life_sciences
Case studies from WUR Modern Statistics for Life Sciences course
stcolema/HumanEyeMovement
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.