This package provides 2 methods for identifying disease-cell type associations: gene set compactness (GSC) and gene set overexpression (GSO). Also provided are functions for recreating the results from Cornish et al.
How to run the methods and recreate the results of Cornish et al. is described in the package vignette. The package manual contains additional information about each of the functions. Both the package vignette and package manual are contained within the package.
Download package binaries
The development version of DiseaseCellTypes can be downloaded and installed using the devtools R-package. DiseaseCellTypes depends on a number of other R-packages, including gplots, igraph, Matrix, psych, snow and stringr.
#install.packages("devtools") require(devtools) install_github("alexjcornish/DiseaseCellTypes")