cytosignal

CytoSignal & VeloCytoSignal

CytoSignal & VeloCytoSignal 是一个可以从空间转录组数据中以细胞分辨率检测静态和动态细胞间信号的工具。

我们的工具适用于大多数基于测序或探针的空间转录组技术，例如 Slide-seq、Stereo-seq 和 MERFISH，

只需要一个细胞-基因矩阵和一个细胞-空间位置矩阵即可。

Installation

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!

Tutorial

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
• Infer differentially signaling interactions across multiple datasets
• Interoperate with Seurat/SingleCellExperiment/anndata
• Using user-customized ligand-receptor interactions

Reproducing Plots from Figures

To reproduce the plots from the main figure panels, please see these notebooks from https://github.com/skpalan/cytosignal-figure:

• Figure 2, a-g
• Figure 2, h-r
• Figure 2, o&k
• Figure 3
• Figure 3c
• Figure 3h
• Figure 4
• Figure 4c
• Figure 5, a-c
• Figure 5, d-g

License

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