README.md

In AlmogAngel/xCell2: A Tool for Generic Cell Type Enrichment Analysis

xCell 2.0: Robust Cell Type Enrichment Analysis

Overview

xCell 2.0 is an advanced R package and web application for cell type enrichment analysis, building upon the widely-used xCell algorithm. It introduces a training function that allows the utilization of custom reference datasets, making it adaptable to diverse tissue types and experimental conditions.

Installation

The package is currently available on GitHub and is being prepared for Bioconductor submission:

devtools::install_github('AlmogAngel/xCell2')
library(xCell2)

Important Notes

• xCell 2.0 produces enrichment scores, not percentages. It's designed for comparing across samples, not cell types.
• xCell 2.0 requires variability among samples for accurate linear transformation.
• The method is designed for mixed samples, not for determining cell of origin or single-cell analysis.

Vignettes

Introduction to Cell Type Enrichment Analysis with xCell 2.0

Contributors

xCell 2.0 is developed by the Aran lab at the Technion - Israel Institute of Technology. Contact: Almog Angel (almog.angel at campus.technion.ac.il) Dvir Aran (dvir.aran at technion.ac.il)

Citation

If you use xCell 2.0 in your research, please cite our paper: Angel A, Naom L, Nabel-Levy S, Aran D. xCell 2.0: Robust Algorithm for Cell Type Proportion Estimation Predicts Response to Immune Checkpoint Blockade. bioRxiv 2024.

License

GLP 3.0

AlmogAngel/xCell2 documentation built on Oct. 14, 2024, 4:51 a.m.