scDiffCom
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CyrilLagger
Difference in Intercellular Communication from scRNA-seq data
scDiffCom
scDiffCom stands for “single-cell Differential Communication” and infers changes in intercellular communication between two biological conditions from scRNA-seq data (as 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
# 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 and this vignette.
For a concrete and large-scale project that used scDiffCom, please look at scagecom.org, our murine atlas of age-related changes in intercellular communication.
Citation
Please consider reading and citing our Nature Aging paper: here.
Metadata
Owner
CyrilLagger
Metadata
Difference in Intercellular Communication from scRNA-seq data