Software & Tools

xCell is a gene signatures-based method for inferring 64 immune and stromal cell types from gene expression data. It applies a novel technique for reducing associations between closely related cell types, producing a more accurate portrayal of the tissue cellular heterogeneity landscape. Used by over 20,000 researchers worldwide.

xCell 2.0 is a major update that provides robust cell type proportion estimation from bulk RNA-seq data. It features improved accuracy, new reference profiles, and the ability to predict response to immune checkpoint blockade treatments based on the tumor microenvironment cellular composition.

SingleR is an automatic annotation method for single-cell RNA-seq data. It leverages reference transcriptomic datasets of pure cell types to independently infer the cell type identity of each cell in a given single-cell dataset. Installed over 10,000 times from Bioconductor since September 2019.

CellMentor provides cell-type aware dimensionality reduction that preserves biological structure in single-cell data, enabling better visualization and downstream analysis.

SLAYER is a computational framework that identifies synthetic lethal interactions by integrating multiple cancer dependency datasets, providing insights for targeted cancer therapy development.