https://github.com/BlishLab/scriabin

Analysis of cell-cell communication at single-cell resolution
https://github.com/BlishLab/scriabin

Last synced: 4 months ago
JSON representation

Analysis of cell-cell communication at single-cell resolution

• Host: GitHub
• URL: https://github.com/BlishLab/scriabin
• Owner: BlishLab
• License: other
• Created: 2021-12-15T16:29:22.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2023-08-18T18:23:59.000Z (10 months ago)
• Last Synced: 2024-01-14T19:43:36.125Z (5 months ago)
• Language: R
• Size: 8.35 MB
• Stars: 91
• Watchers: 6
• Forks: 10
• Open Issues: 10
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Lists

• awesome-cell-cell-communication - scriabin - [R]- scriabin aims to provide a comprehensive view of cell-cell communication at the single-cell level without requiring subsampling or aggregation. (Uncategorized / Uncategorized)

README

        
# scriabin

Single-cell resolution interaction analysis through binning

NB 23 June 2023: I am currently the only person maintaining this package and am in medical school rotations. I appreciate your patience as there may be times I respond slowly to issues that are opened. 

## Goal

Scriabin aims to provide a comprehensive view of cell-cell communication (CCC) at the single-cell level without requiring subsampling or aggregation. 

## Summary

Scriabin is a computational framework for analysis of cell-cell communication at single-cell resolution. Scriabin consists of 3 main workflows depending on dataset size and analytical goals: 1. the cell-cell interaction matrix workflow, optimal for smaller datasets, analyzes communication methods used for each cell-cell pair in the dataset; 2. the summarized interaction graph workflow, designed for large comparative analyses, identifies cell-cell pairs with different total communicative potential between samples; and, 3) the interaction program discovery workflow, suitable for any dataset size, finds modules of co-expressed ligand-receptor pairs. 

## Installation

Scriabin is implemented in R. To install: 

```

devtools::install_github("BlishLab/scriabin", ref = "main")

```

## Vignettes

Vignettes are available in the vignettes directory of this repo.