csSAM

This package implements the method csSAM that computes cell-specific differential expression from measured cell proportions using SAM, as described in:

Cell type-specific gene expression differences in complex tissues
Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM and Butte AJ
Nature methods, 7(4), pp. 287–9. ISSN 1548-7105 10.1038/nmeth.1439

Installation

# install package devtools if necessary
install.packages('devtools')

# install csSAM
devtools::install_github('shenorlab/csSAM')