CellChat

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.

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.

Spatially resolved gene expression profiles are key to understand tissue organization and function. However, spatial transcriptomics (ST) profiling techniques lack single-cell resolution and require a combination with single-cell RNA sequencing (scRNA-seq) information to deconvolute the spatially indexed datasets. Leveraging the strengths of both data types, we developed SPOTlight, a computational tool that enables the integration of ST with scRNA-seq data to infer the location of cell types and states within a complex tissue. SPOTlight is centered around a seeded non-negative matrix factorization (NMF) regression, initialized using cell-type marker genes and non-negative least squares (NNLS) to subsequently deconvolute ST capture locations (spots). Simulating varying reference quantities and qualities, we confirmed high prediction accuracy also with shallowly sequenced or small-sized scRNA-seq reference datasets. SPOTlight deconvolution of the mouse brain correctly mapped subtle neuronal cell states of the cortical layers and the defined architecture of the hippocampus. In human pancreatic cancer, we successfully segmented patient sections and further fine-mapped normal and neoplastic cell states. Trained on an external single-cell pancreatic tumor references, we further charted the localization of clinical-relevant and tumor-specific immune cell states, an illustrative example of its flexible application spectrum and future potential in digital pathology.

The recent development of single-cell RNA-sequencing (scRNA-seq) technology has enabled us to infer cell-type-specific co-expression networks, enhancing our understanding of cell-type-specific biological functions. However, existing methods proposed for this task still face challenges due to unique characteristics in scRNA-seq data, such as high sequencing depth variations across cells and measurement errors. CS-CORE (Su, C., Xu, Z., Shan, X. et al., 2023), an R package for cell-type-specific co-expression inference, explicitly models sequencing depth variations and measurement errors in scRNA-seq data. In this notebook, we will illustrate an example workflow of CS-CORE using a dataset of Peripheral Blood Mononuclear Cells (PBMC) from COVID patients and healthy controls (Wilk et al., 2020). The notebook content is inspired by CS-CORE's vignette and modified to demonstrate how the tool works on BioTuring's platform.