- spicyR (http://www.bioconductor.org/packages/release/bioc/html/spicyR.html)
Provides a series of functions to aid in the analysis of both immunofluorescence and mass cytometry imaging data as well as other assays that can deeply phenotype individual cells and their spatial location.
- AFid (https://ellispatrick.github.io/AFid/)
A method implemented in ImageJ, Matlab and R that identifies and removes autofluorescent signals from multi-channel images post acquisition.
- 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.