CellChat

scVI-tools (single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data primarily developed and maintained by the Yosef Lab at UC Berkeley. scvi-tools has two components - Interface for easy use of a range of probabilistic models for single-cell omics (e.g., scVI, scANVI, totalVI). - Tools to build new probabilistic models, which are powered by PyTorch, PyTorch Lightning, and Pyro.

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.

Single-cell RNA sequencing methods can profile the transcriptomes of single cells but cannot preserve spatial information. Conversely, spatial transcriptomics assays can profile spatial regions in tissue sections but do not have single-cell resolution. Here, Runmin Wei (Siyuan He, Shanshan Bai, Emi Sei, Min Hu, Alastair Thompson, Ken Chen, Savitri Krishnamurthy & Nicholas E. Navin) developed a computational method called CellTrek that combines these two datasets to achieve single-cell spatial mapping through coembedding and metric learning approaches. They benchmarked CellTrek using simulation and in situ hybridization datasets, which demonstrated its accuracy and robustness. They then applied CellTrek to existing mouse brain and kidney datasets and showed that CellTrek can detect topological patterns of different cell types and cell states. They performed single-cell RNA sequencing and spatial transcriptomics experiments on two ductal carcinoma in situ tissues and applied CellTrek to identify tumor subclones that were restricted to different ducts, and specific T-cell states adjacent to the tumor areas.

Classification of tumor and normal cells in the tumor microenvironment from scRNA-seq data is an ongoing challenge in human cancer study. Copy number karyotyping of aneuploid tumors (***copyKAT***) (Gao, Ruli, et al., 2021) is a method proposed for identifying copy number variations in single-cell transcriptomics data. It is used to predict aneuploid tumor cells and delineate the clonal substructure of different subpopulations that coexist within the tumor mass. In this notebook, we will illustrate a basic workflow of CopyKAT based on the tutorial provided on CopyKAT's repository. We will use a dataset of triple negative cancer tumors sequenced by 10X Chromium 3'-scRNAseq (GSM4476486) as an example. The dataset contains 20,990 features across 1,097 cells. We have modified the notebook to demonstrate how the tool works on BioTuring's platform.