https://github.com/CyrilLagger/scDiffCom

Difference in Intercellular Communication from scRNA-seq data
https://github.com/CyrilLagger/scDiffCom

Last synced: 4 months ago
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Difference in Intercellular Communication from scRNA-seq data

• Host: GitHub
• URL: https://github.com/CyrilLagger/scDiffCom
• Owner: CyrilLagger
• License: other
• Created: 2020-04-04T18:59:38.000Z (about 4 years ago)
• Default Branch: master
• Last Pushed: 2024-01-02T00:14:19.000Z (6 months ago)
• Last Synced: 2024-01-03T01:47:54.447Z (6 months ago)
• Language: R
• Homepage: https://cyrillagger.github.io/scDiffCom
• Size: 54.6 MB
• Stars: 16
• Watchers: 4
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE

Lists

• awesome-cell-cell-communication - scDiffCom - [R]- scDiffCom stands for “single-cell Differential Communication” and infers changes in intercellular communication between two biological conditions from scRNA-seq data. (Uncategorized / Uncategorized)

README

        
---

output: github_document

---

```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```

# scDiffCom

[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)

[![CRAN status](https://www.r-pkg.org/badges/version/scDiffCom)](https://CRAN.R-project.org/package=scDiffCom)

[![Codecov test coverage](https://codecov.io/gh/CyrilLagger/scDiffCom/branch/master/graph/badge.svg)](https://app.codecov.io/gh/CyrilLagger/scDiffCom?branch=master)

[![R-CMD-check](https://github.com/CyrilLagger/scDiffCom/workflows/R-CMD-check/badge.svg)](https://github.com/CyrilLagger/scDiffCom/actions)

scDiffCom stands for "single-cell Differential Communication" and infers 

changes in intercellular communication between two biological 

conditions from scRNA-seq data (as [Seurat](https://satijalab.org/seurat/)

objects). The package relies on an internal collection of ligand-receptor 

interactions (available for human, mouse and rat) retrieved from seven 

curated databases.

Display LRI databases

* [CellChat](http://www.cellchat.org/)

* [CellPhoneDB](https://www.cellphonedb.org/)

* [CellTalkDB](http://tcm.zju.edu.cn/celltalkdb/)

* [connectomeDB2020](https://github.com/forrest-lab/NATMI)

* [ICELLNET](https://github.com/soumelis-lab/ICELLNET)

* [NicheNet](https://github.com/saeyslab/nichenetr)

* [SingleCellSignalR](https://www.bioconductor.org/packages/release/bioc/html/SingleCellSignalR.html)

 

## Installation

``` r

# Install the development version from GitHub

devtools::install_github("CyrilLagger/scDiffCom")

# Install release version from CRAN

install.packages("scDiffCom")

```

## Usage

As an introduction, please look at the

[documentation](https://cyrillagger.github.io/scDiffCom/) and this [vignette](https://cyrillagger.github.io/scDiffCom/articles/scDiffCom-vignette.html).

For a concrete and large-scale project that used scDiffCom, please look at

[scagecom.org](https://scagecom.org/), our murine atlas of

age-related changes in intercellular communication.

## Citation

Please consider reading and citing our Nature Aging paper:

[here](https://www.nature.com/articles/s43587-023-00514-x).