GitHub - AlmogAngel/xCell2: xCell 2.0: Robust Cell Type Enrichment Analysis (original) (raw)
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:
- 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.
- 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.
- 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 to3838
.
* Leave all other fields as default. - Click Run to start the container.
- 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, 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