E-spatial

Charting an organs’ biological atlas requires us to spatially resolve the entire single-cell transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and single-nucleus RNA-seq (sc/snRNA-seq) can profile cells comprehensively, but lose spatial information. Spatial transcriptomics allows for spatial measurements, but at lower resolution and with limited sensitivity. Targeted in situ technologies solve both issues, but are limited in gene throughput. To overcome these limitations we present Tangram, a method that aligns sc/snRNA-seq data to various forms of spatial data collected from the same region, including MERFISH, STARmap, smFISH, Spatial Transcriptomics (Visium) and histological images. **Tangram** can map any type of sc/snRNA-seq data, including multimodal data such as those from SHARE-seq, which we used to reveal spatial patterns of chromatin accessibility. We demonstrate Tangram on healthy mouse brain tissue, by reconstructing a genome-wide anatomically integrated spatial map at single-cell resolution of the visual and somatomotor areas.

In the realm of transcriptional dynamics, understanding the intricate interplay of regulatory proteins is crucial for deciphering processes ranging from normal development to disease progression. However, traditional RNA velocity methods often overlook the underlying regulatory drivers of gene expression changes over time. This gap in knowledge hinders our ability to unravel the mechanistic intricacies of these dynamic processes. scKINETICs (Key regulatory Interaction NETwork for Inferring Cell Speed) (Burdziak et al, 2023) offers a dynamic model for gene expression changes that simultaneously learns per-cell transcriptional velocities and a governing gene regulatory network. By employing an expectation-maximization approach, scKINETICS quantifies the impact of each regulatory element on its target genes, incorporating insights from epigenetic data, gene-gene coexpression patterns and constraints dictated by the phenotypic manifold.

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.

Power analyses are considered important factors in designing high-quality experiments. However, such analyses remain a challenge in single-cell RNA-seq studies due to the presence of hierarchical structure within the data (Zimmerman et al., 2021). As cells sampled from the same individual share genetic and environmental backgrounds, these cells are more correlated than cells sampled from different individuals. Currently, most power analyses and hypothesis tests (e.g., differential expression) in scRNA-seq data treat cells as if they were independent, thus ignoring the intra-sample correlation, which could lead to incorrect inferences. Hierarchicell (Zimmerman, K.D. and Langefeld, C.D., 2021) is an R package proposed to estimate power for testing hypotheses of differential expression in scRNA-seq data while considering the hierarchical correlation structure that exists in the data. The method offers four important categories of functions: data loading and cleaning, empirical estimation of distributions, simulating expression data, and computing type 1 error or power. In this notebook, we will illustrate an example workflow of Hierarchicell. The notebook is inspired by Hierarchicell's vignette and modified to demonstrate how the tool works on BioTuring's platform.