This is a custom version of the package talkLR which allows the usage of custom Ligand Receptor interaction resource.
talklr (intercellular crossTALK using Ligand-Receptor)uses Kullback-Leibler divergence, a concept from inforamtion theory, to uncover interesting ligand-receptor interactions among multiple cell types in single cell RNA-seq data.
This is an R package for talklr, so that you can integrate talklr analysis into your any existing scRNA-seq bioinformatic workflow.
To install talklr R package, you need to first install the devltools R package, then run:
library(devtools)
install_github("yuliangwang/talklr")
library(talklr)You can follow the tutorial below to get started using talklr on your single cell RNA-seq data (or bulk RNA-seq of purified cells):
https://rpubs.com/wang341/570900
Now talklr is ready for use!
Alternatively, you can use the talklr Shiny App that does not require any programming experience. talklr App is available at:
https://yuliangwang.shinyapps.io/talklr/
If you use talklr in your work, please cite the paper below:
Yuliang Wang. (2020). talklr uncovers ligand-receptor mediated intercellular crosstalk. bioRxiv, 2020.02.01.930602. doi:10.1101/2020.02.01.930602