CytoSignal & VeloCytoSignal is a tool for detecting static and dynamic cell-cell signaling at cellular resolution from spatial transcriptomic data. Our tools are applicable to most sequencing-based and probe-based spatial transcriptomic techniques, such as Slide-seq, Stereo-seq, and MERFISH, requiring only a cell-by-gene matrix and a cell-by-spatial-position matrix.

Check out our paper for a more complete description of the methods and analyses:

Jialin Liu, Hiroaki Manabe, Weizhou Qian, Yichen Wang, Yichen Gu, Angel Ka Yan Chu, Gaurav Gadhvi, Yuxuan Song, Noriaki Ono, Joshua D Welch, CytoSignal Detects Locations and Dynamics of Ligand-Receptor Signaling at Cellular Resolution from Spatial Transcriptomic Data, 2024, bioRxiv, DOI: 10.1101/2024.03.08.584153

The package is developed and tested under R>=4.2.0. Users can install R following the instruction provided on CRAN. To install CytoSimplex & VelcoCytoSignal in R, run the following command in an R console:

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("welch-lab/cytosignal")

We are currently working on releasing a CRAN version. Stay tuned!

For usage examples and guided walkthroughs, check the vignettes directory of the repo.

• Infer spatially resolved cell-cell communication signaling at cellular resolution
• Infer spatially resolved temporal dynamics of cell-cell communication at cellular resolution

This project is covered under the GNU General Public License 3.0.