R packages

  • sydSeq (
    An R package containing the functions exClust, TshrinkPlus and pMim. An example illustrating how to use pMim can be found here.

  • directPA (
    A package for pathway analysis in experiments with multiple perturbation designs. For more information about this package please see our publication.

  • edgeBundleR (
    A package that Garth and I wrote for plotting a circular network graph with “bundled” edges. This package allows R users to easily create a hierarchical edge bundle plot. The underlying D3 code was adapted from Mike Bostock’s examples (see here or here) and the package is based on the htmlwidgets framework.

Shiny applications

  • MicrogliaPlots A shiny application for exploring the expression of genes in human microglia from an aged population.