xCell is a webtool that performs cell type enrichment analysis from gene expression data for 64 immune and stroma cell types.
xCell is a gene signatures-based method learned from thousands of pure cell types from various sources. xCell applies a novel technique for reducing associations between closley related cell types. xCell signatures were validated using extensive in-silico simulations and also cytometry immunophenotyping, and were shown to outperform previous methods. xCell allows researchers to reliably portray the cellular heterogeneity landscape of tissue expression profiles.
For more informations please refer to the xCell manuscript.
library(xCell)
exprMatrix = read.table(expr_file,header=TRUE,row.names=1, as.is=TRUE)
xCellAnalysis(exprMatrix)
devtools::install_github('dviraran/xCell')
xCell is developed by the Butte lab. Please contact Dvir Aran: dvir.aran at ucsf edu for any questions or suggestions.
To cite xCell: Aran, Hu and Butte, xCell: Digitally portraying the tissue cellular heterogeneity landscape. bioRxiv, 2017