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VCCRI / scTalk

Intercellular communication analysis for scRNA-seq data
GNU General Public License v3.0
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intercellular-communication ligand-receptor scrna-seq scrna-seq-analysis

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scTalk

scTalk is an R package for intercellular communication (ligand-receptor) analysis from scRNA-seq data and implements the method described in Farbehi et al.. Please read the vignette for an explanation of how to use the software.

Installation

To install scTalk, open an R session and use the following commands:

install.packages("devtools")
devtools::install_github("VCCRI/scTalk", build = TRUE, build_vignettes = TRUE, build_opts = c("--no-resave-data", "--no-manual"))

To access the vignette:

library(scTalk)
browseVignettes("scTalk")

Citation

If you find scTalk useful in your research, please cite the following paper:

Farbehi N, Patrick R, Dorison A, Xaymardan M, Janbandhu V, Wystub-Lis K, Ho JWK, Nordon RE, and Harvey RP. Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury. eLife, 8:e43882, 2019.