cytosignal-figure

This is a repository for notebooks and the corresponding data needed to reproduce the main figures from the CytoSignal paper.

If you’re interested, check out our main CytoSignal repo for the downloadable software.

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

Tutorial

To reproduce all the figures, check out the notebooks below. Please note that all data used in the notebooks are located in the data directory. Due to the data sizes, CytoSignal objects of all datasets named cs_obj_xxx are published and stored on Zenodo: Part 1 and Part 2. Raw data of our VisiumHD data is stored on GEO.

• 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