ShinyCC: A Shiny App for Cell-Cell Communication Analysis

Introduction

ShinyCC is a Shiny app built on top of the CellChat package by Songqi Jin. This app provides an interactive interface for analyzing cell-cell communication from single-cell RNA-seq data. The app simplifies the process of comparing interactions across different conditions and visualizing communication networks, making it easier for users to interpret their results.

Key Features

• Visualization of Cell-Cell Communication: Generate plots to visualize the number of interactions or interaction strength across different conditions.
• Comparison Between Conditions: Easily compare cell-cell communication across multiple samples or conditions.
• Customizable Plots: Adjust plot dimensions, label sizes, and more to suit your needs.
• Real-Time Memory Monitoring: Ensure smooth app performance by monitoring memory usage and receiving warnings when memory is critically high.

Reference

This Shiny app is built using the CellChat package by Songqi Jin. For more details on the original package, please visit the CellChat GitHub repository.

Package Dependencies

To run this Shiny app, you'll need the following R packages installed:

• shiny
• shinycssloaders
• dplyr
• shinythemes
• shinyWidgets
• pryr
• CellChat (v2)

You can install these packages using the following commands:

install.packages(c("shiny", "shinycssloaders", "dplyr", "shinythemes", "shinyWidgets", "pryr"))
# Install CellChat from GitHub
devtools::install_github("sqjin/CellChat")

Note that when building the shiny app for Shiny Server or shinyapps.io, you will need to delete the "*.o" files in /src/ because they will prevent the package from correctly compiling. To do so, you may either fork the original repository and delete those files yourself, or install my forked version through devtools::install_github("mianaz/CellChat"). A locally installed version will not work for shinyapps.io.

Input Requirements

The app requires a pre-processed CellChat object that includes the results of cell-cell communication analysis. The CellChat object should be merged if multiple conditions/samples are to be compared.