An R-package for identifying disease-associated cell types using cell type-specific interactomes. 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.

• Disease-cell type associations
• Cell type-specific interactomes

• Mac OS/X binary
• Windows binary
• Source package

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")

Cornish A.J., Filippis I., David A. and Sternberg M.J.E. (2015) Exploring the cellular basis of human disease through a large-scale mapping of deleterious genes to cell types. Genome Medicine, 7:95