Cell–cell communication mediated by ligand–receptor complexes is critical to coordinating diverse biological processes, such as development, differentiation and inflammation. To investigate how the context-dependent crosstalk of different cell types enables physiological processes to proceed, we developed CellPhoneDB, a novel repository of ligands, receptors and their interactions. In contrast to other repositories, our database takes into account the subunit architecture of both ligands and receptors, representing heteromeric complexes accurately. We integrated our resource with a statistical framework that predicts enriched cellular interactions between two cell types from single-cell transcriptomics data. Here, we outline the structure and content of our repository, provide procedures for inferring cell–cell communication networks from single-cell RNA sequencing data and present a practical step-by-step guide to help implement the protocol. CellPhoneDB v.2.0 is an updated version of our resource that incorporates additional functionalities to enable users to introduce new interacting molecules and reduces the time and resources needed to interrogate large datasets. CellPhoneDB v.2.0 is publicly available, both as code and as a user-friendly web interface; it can be used by both experts and researchers with little experience in computational genomics. In our protocol, we demonstrate how to evaluate meaningful biological interactions with CellPhoneDB v.2.0 using published datasets. This protocol typically takes ~2 h to complete, from installation to statistical analysis and visualization, for a dataset of ~10 GB, 10,000 cells and 19 cell types, and using five threads.

Cell2location is a principled Bayesian model that can resolve fine-grained cell types in spatial transcriptomic data and create comprehensive cellular maps of diverse tissues. Cell2location accounts for technical sources of variation and borrows statistical strength across locations, thereby enabling the integration of single cell and spatial transcriptomics with higher sensitivity and resolution than existing tools. This is achieved by estimating which combination of cell types in which cell abundance could have given the mRNA counts in the spatial data, while modelling technical effects (platform/technology effect, contaminating RNA, unexplained variance). This tutorial shows how to use cell2location method for spatially resolving fine-grained cell types by integrating 10X Visium data with scRNA-seq reference of cell types. Cell2location is a principled Bayesian model that estimates which combination of cell types in which cell abundance could have given the mRNA counts in the spatial data, while modelling technical effects (platform/technology effect, contaminating RNA, unexplained variance).

Single-cell RNA data allows cell-cell communications (***CCC***) methods to infer CCC at either the individual cell or cell cluster/cell type level, but physical distances between cells are not preserved Almet, Axel A., et al., (2021). On the other hand, spatial data provides spatial distances between cells, but single-cell or gene resolution is potentially lost. Therefore, integrating two types of data in a proper manner can complement their strengths and limitations, from that improve CCC analysis. In this pipeline, we analyze CCC on Visium data with single-cell data as a reference. The pipeline includes 4 sub-notebooks as following 01-deconvolution: This step involves deconvolution and cell type annotation for Visium data, with cell type information obtained from a relevant single-cell dataset. The deconvolution method is SpatialDWLS which is integrated in Giotto package. 02-giotto: performs spatial based CCC and expression based CCC on Visium data using Giotto method. 03-nichenet: performs spatial based CCC and expression based CCC on Visium data using NicheNet method. 04-visualization: visualizes CCC results obtained from Giotto and NicheNet.