This is my personal blog. I’ll do my best to keep it updated but I make no promises! Posts are likely to be a mix of programming, data visualisation, statistics and personal topics.

Pages

• About me

• Curriculum vitae

Blog posts

• Immunity passports and Bayes theorem (08 April 2020) - stats and Bayes by dummies

• Bayesian regression by dummy (22 March 2020) - stats and Bayes by dummies

• Modelling disease mortality (30 January 2020) - stats and Bayes by dummies

• Visualising data with R, htmlwidgets, and Javascript (28 November 2019) - programming and data visualisation

• Jekyll and Rmarkdown (the wrong way) (14 November 2018) - programming and data visualisation

• Dulce Et Decorum Est (11 November 2018) - personal

Package sites

Here are some links to R packages I’ve written or contributed to:

• CRAN packages:

  Package	Description	Version	Downloads
  heatmaply	Interactive cluster heatmaps in R.
  contrast	Contrasts for linear models in R.
  bayefdr	Bayesian estimation and optimisation of expected FDR and expected FNR.

• Bioconductor:

  Package	Description	Devel	Release	Rank
  scater	Single cell analysis toolkit.
  BASiCS	Bayesian model for analysis of single-cell sequencing data.
  snifter	R wrapper for the python openTSNE library implementing fast interpolated t-SNE.
  densvis	Density-preserving non-linear dimensionality reduction methods.

• Misc:
  • heatmaplyExamples:
    Vignettes demonstrating the utility of heatmaply for various applications
  • plotlyutils:
    Some functions for creating nice interactive plots using the plotly R and JS libraries.
  • nalar:
    A personal R library I use for common analysis tasks. May be published on CRAN eventually.
  • plotlyvignettes:
    Vignettes relating to my plotlyutils package. Was used as the basis for a talk at an Edinburgh Bioinformatics meeting (2018-11-08).

• Teaching materials:
  I have also contributed to and maintain some teaching materials:

  Name	Website	Source
  High dimensional statistics with R	Carpentries Incubator	GitHub
  Orchestrating single cell analysis (landing)	Bioconductor	GitHub
  Orchestrating single cell analysis (multisample)	Bioconductor	GitHub