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<img src="man/figures/xcell2logo.png" width="30%">
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# 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:
```R
devtools::install_github('AlmogAngel/xCell2')
library(xCell2)
```
Install via [Bioconductor](https://bioconductor.org/packages/devel/bioc/html/xCell2.html) (development version):
```
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("xCell2")
```
## Vignettes
[Introduction to Cell Type Enrichment Analysis with xCell 2.0](https://aran-lab.com/xcell2-vignette)
## 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/](https://docs.docker.com/get-docker/).
- Open Docker Desktop and make sure it is running.
<small>\* If you already have Docker Desktop installed, you might need to update it to the latest version.</small>
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](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.
<img src="man/figures/xcell2_shiny.png">
## 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.](https://doi.org/10.1101/2024.09.06.611424)
## License
GLP 3.0
