In dviraran/xCell: Cell type enrichment analysis

Tissues are a complex milieu consisting of numerous cell types. In cancer, understanding the cellular heterogeneity in the tumor microenvironment is an emerging field of research. Numerous methods have been published in recent years for the enumeration of cell subsets from tissue expression profiles. However, the available methods suffer from three major problems: inferring cell subset based on gene sets learned and verified from limited sources; displaying only partial portrayal of the full cellular heterogeneity; and insufficient validation in mixed tissues.

xCell is a tool 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.

To use xCell simply load a human gene expression data matrix. The rows of the matrix must be gene symbols. If the data contains non-unique gene symbols, rows with same gene symbols will be averaged.

dviraran/xCell documentation built on Nov. 22, 2020, 7:24 p.m.