In this notebook, we present COMMOT (COMMunication analysis by Optimal Transport) to infer cell-cell communication (CCC) in spatial transcriptomic, a package that infers CCC by simultaneously considering numerous ligand–receptor pairs for either spatial transcriptomic data or spatially annotated scRNA-seq data equipped with spatial distances between cells estimated from paired spatial imaging data. A collective optimal transport method is developed to handle complex molecular interactions and spatial constraints. Furthermore, we introduce downstream analysis tools to infer spatial signaling directionality and genes regulated by signaling using machine learning models.

Spatial transcriptomics (ST) technology has allowed to capture of topographical gene expression profiling of tumor tissues, but single-cell resolution is potentially lost. Identifying cell identities in ST datasets from tumors or other samples remains challenging for existing cell-type deconvolution methods. Spatial Cellular Estimator for Tumors (SpaCET) is an R package for analyzing cancer ST datasets to estimate cell lineages and intercellular interactions in the tumor microenvironment. Generally, SpaCET infers the malignant cell fraction through a gene pattern dictionary, then calibrates local cell densities and determines immune and stromal cell lineage fractions using a constrained regression model. Finally, the method can reveal putative cell-cell interactions in the tumor microenvironment. In this notebook, we will illustrate an example workflow for cell type deconvolution and interaction analysis on breast cancer ST data from 10X Visium. The notebook is inspired by SpaCET's vignettes and modified to demonstrate how the tool works on BioTuring's platform.

CellRank2 (Weiler et al, 2023) is a powerful framework for studying cellular fate using single-cell RNA sequencing data. It can handle millions of cells and different data types efficiently. This tool can identify cell fate and probabilities across various data sets. It also allows for analyzing transitions over time and uncovering key genes in developmental processes. Additionally, CellRank2 estimates cell-specific transcription and degradation rates, aiding in understanding differentiation trajectories and regulatory mechanisms. In this notebook, we will use a primary tumor sample of patient T71 from the dataset GSE137804 (Dong R. et al, 2020) as an example. We have performed RNA-velocity analysis and pseudotime calculation on this dataset in scVelo (Bergen et al, 2020) notebook. The output will be then loaded into this CellRank2 notebook for further analysis. This notebook is based on the tutorial provided on CellRank2 documentation. We have modified the notebook and changed the input data to show how the tool works on BioTuring's platform.