Software

R packages


  • sydSeq (https://github.com/ellispatrick/sydSeq/)
    An R package containing the functions exClust, TshrinkPlus and pMim. An example illustrating how to use pMim can be found here.

  • directPA (http://cran.r-project.org/web/packages/directPA/)
    A package for pathway analysis in experiments with multiple perturbation designs. For more information about this package please see our publication.

  • edgeBundleR (https://cran.r-project.org/web/packages/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.