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

Install via GitHub:

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

Install via Bioconductor:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("xCell2")

Vignettes

Introduction to Cell Type Enrichment Analysis with xCell 2.0

Using xCell 2.0 with a User Interface (No Code Required)

You can now run xCell 2.0 with a simple and user-friendly interface using Docker Desktop, no coding required.

Follow these steps:

1. Install Docker Desktop
   • *Download and install Docker Desktop from https://docs.docker.com/get-docker/.
   • Open Docker Desktop and make sure it is running.

* If you already have Docker Desktop installed, you might need to update it to the latest version.

2. Pull the xCell 2.0 Docker Image
   • Navigate to the Search bar on the top.
   • Enter the following in the "Images" field:
     almogangel/xcell2
   • Click Pull and wait for the image to download.

3. Run the xCell 2.0 App
   • Once the image is downloaded, find it under the Images tab in Docker Desktop.
   • Click the Run button next to the almogangel/xcell2:latest image.
   • In the pop-up window:
     • Go to Optional settings.
     • Set Host Port to 3838.
     • Leave all other fields as default.
   • Click Run to start the container.

4. Access the App
   • Open your web browser and go to http://localhost:3838.
   • Start analyzing your data with the intuitive xCell 2.0 interface!
   • When you are done, go back to Docker Desktop and Stop the image.

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., Nabet-Levy, S. et al. xCell 2.0: robust algorithm for cell type proportion estimation predicts response to immune checkpoint blockade. Genome Biol 26, 335 (2025)

License

GLP 3.0