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xcell2

xCell 2.0: Robust Cell Type Enrichment Analysis

https://github.com/almogangel/xcell2

Science Score: 39.0%

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    CITATION.cff file
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    Found codemeta.json file
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    Found .zenodo.json file
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    DOI references
    Found 2 DOI reference(s) in README
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    Academic publication links
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    Scientific vocabulary similarity
    Low similarity (17.4%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

xCell 2.0: Robust Cell Type Enrichment Analysis

Basic Info
  • Host: GitHub
  • Owner: AlmogAngel
  • License: gpl-3.0
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 27.1 MB
Statistics
  • Stars: 9
  • Watchers: 1
  • Forks: 3
  • Open Issues: 3
  • Releases: 0
Created over 4 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog License

README.md

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: ``` 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

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

  1. 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.

  1. 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.

  1. 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

Owner

  • Name: Almog Angel
  • Login: AlmogAngel
  • Kind: user

PhD candidate at Technion - Israel Institute of Technology

GitHub Events

Total
  • Issues event: 22
  • Watch event: 5
  • Issue comment event: 29
  • Push event: 48
  • Pull request review event: 1
  • Pull request event: 2
  • Fork event: 1
Last Year
  • Issues event: 22
  • Watch event: 5
  • Issue comment event: 29
  • Push event: 48
  • Pull request review event: 1
  • Pull request event: 2
  • Fork event: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 13
  • Total pull requests: 1
  • Average time to close issues: about 1 month
  • Average time to close pull requests: about 11 hours
  • Total issue authors: 10
  • Total pull request authors: 1
  • Average comments per issue: 1.62
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 13
  • Pull requests: 1
  • Average time to close issues: about 1 month
  • Average time to close pull requests: about 11 hours
  • Issue authors: 10
  • Pull request authors: 1
  • Average comments per issue: 1.62
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Rohit-Satyam (2)
  • hoeflerb (2)
  • bsb2014 (2)
  • 4ndr34-1t (1)
  • humtn (1)
  • swolfsci (1)
  • lindseydruschel (1)
  • Shubhra-B (1)
  • hsiaoyi0504 (1)
  • ndaniel (1)
Pull Request Authors
  • vjcitn (1)
  • PeteHaitch (1)
Top Labels
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Dependencies

DESCRIPTION cran
  • R >= 2.10 depends
  • GSEABase * imports
  • Rfast * imports
  • Seurat * imports
  • dplyr * imports
  • ontoProc * imports
  • ontologyIndex * imports
  • plyr * imports
  • singscore * imports
  • sparseMatrixStats * imports
  • tibble * imports