Software

R packages


  • DCARS (https://github.com/shazanfar/DCARS/)
    An R package for performing differential correlation across ranked samples developed by Shila Ghazanfar.

  • dialects (https://github.com/madeleineotway/dialects/)
    An R package for converting SWATH-MS spectral reference libraries (SRLs) between species developed by Madeleine Otway.

  • directPA (http://cran.r-project.org/web/packages/directPA/)
    An R 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)
    An R package that Garth Tarr 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.

  • 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.


Shiny applications

  • dialects A shiny application for converting SWATH-MS spectral reference libraries (SRLs) between species.
  • MicrogliaPlots A shiny application for exploring the expression of genes in human microglia from an aged population.