E-spatial

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.

Build single-cell trajectories with the software that introduced **pseudotime**. Find out about cell fate decisions and the genes regulated as they're made. Group and classify your cells based on gene expression. Identify new cell types and states and the genes that distinguish them. Find genes that vary between cell types and states, over trajectories, or in response to perturbations using statistically robust, flexible differential analysis. In development, disease, and throughout life, cells transition from one state to another. Monocle introduced the concept of **pseudotime**, which is a measure of how far a cell has moved through biological progress. Many researchers are using single-cell RNA-Seq to discover new cell types. Monocle 3 can help you purify them or characterize them further by identifying key marker genes that you can use in follow-up experiments such as immunofluorescence or flow sorting. **Single-cell trajectory analysis** shows how cells choose between one of several possible end states. The new reconstruction algorithms introduced in Monocle 3 can robustly reveal branching trajectories, along with the genes that cells use to navigate these decisions.

Tumors are complex tissues of cancerous cells surrounded by a heterogeneous cellular microenvironment with which they interact. Single-cell sequencing enables molecular characterization of single cells within the tumor. However, cell annotation—the assignment of cell type or cell state to each sequenced cell—is a challenge, especially identifying tumor cells within single-cell or spatial sequencing experiments. Here, we propose ikarus, a machine learning pipeline aimed at distinguishing tumor cells from normal cells at the single-cell level. We test ikarus on multiple single-cell datasets, showing that it achieves high sensitivity and specificity in multiple experimental contexts. **InferCNV** is a Bayesian method, which agglomerates the expression signal of genomically adjointed genes to ascertain whether there is a gain or loss of a certain larger genomic segment. We have used **inferCNV** to call copy number variations in all samples used in the manuscript.

Understanding global communications among cells requires accurate representation of cell-cell signaling links and effective systems-level analyses of those links. We construct a database of interactions among ligands, receptors and their cofactors that accurately represent known heteromeric molecular complexes. We then develop **CellChat**, a tool that is able to quantitatively infer and analyze intercellular communication networks from single-cell RNA-sequencing (scRNA-seq) data. CellChat predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Through manifold learning and quantitative contrasts, CellChat classifies signaling pathways and delineates conserved and context-specific pathways across different datasets. Applying **CellChat** to mouse and human skin datasets shows its ability to extract complex signaling patterns.