Codon pair optimisation

Optimising genes with a genetic algorithm.

Matplotlib cmap

Simple demos of matplotlib's cmaps.

Flu subtypes

How is the flu sequence data distributed across subtypes, hosts and countries on the NCBI data base?

Confusion matrix

When reporting binary classification models, just looking at accuracy doesn't give the full picture. You need sensitivity & specificity, or precision & recall.

ggtree samples

Code snippets for various ggtree examples.

Ordinal GLM

When a response variable is ordered categories you can predict all categories using a single proportional odds model, instead of separate logistic regression models.

Phylogenetic mixed modelling

Simulate data for a phylogenetic mixed model using a phylogenetic tree to impose the phylogenetic covariance structure.

Gaussian mixture

Unsuperivsed classification based on bivariate data using a gaussian mixture model.

Power & resolution

When binning a continuous variable, e.g. into high and low, positive and negative, you lose information and statistical power.

Additive mixed modelling

Fitting an additive mixed model to account for both long an short term effects of time while fitting an autocorrelation structure to the residuals.

Gaussian process

Fitting a gaussian process to time series data. Using this approach domain knowledge can be used to choose an appropriate covariance function.

Graphic Cite

Web scraping, analysing, and interactive visualisations of data on scientific publishing.

The Denatured

A pop science outreach website produced by a small team of writers and vloggers which I organise.

Jupyter Slides

Easily turn your code, workflow, and results into a presentation. This is great for sharing results with or without your code.