E-spatial

Advances in multi-omics have led to an explosion of multimodal datasets to address questions from basic biology to translation. While these data provide novel opportunities for discovery, they also pose management and analysis challenges, thus motivating the development of tailored computational solutions. `muon` is a Python framework for multimodal omics. It introduces multimodal data containers as `MuData` object. The package also provides state of the art methods for multi-omics data integration. `muon` allows the analysis of both unimodal omics and multimodal omics.

CellRank2 (Weiler et al, 2023) is a powerful framework for studying cellular fate using single-cell RNA sequencing data. It can handle millions of cells and different data types efficiently. This tool can identify cell fate and probabilities across various data sets. It also allows for analyzing transitions over time and uncovering key genes in developmental processes. Additionally, CellRank2 estimates cell-specific transcription and degradation rates, aiding in understanding differentiation trajectories and regulatory mechanisms. In this notebook, we will use a primary tumor sample of patient T71 from the dataset GSE137804 (Dong R. et al, 2020) as an example. We have performed RNA-velocity analysis and pseudotime calculation on this dataset in scVelo (Bergen et al, 2020) notebook. The output will be then loaded into this CellRank2 notebook for further analysis. This notebook is based on the tutorial provided on CellRank2 documentation. We have modified the notebook and changed the input data to show how the tool works on BioTuring's platform.

Single-cell RNA sequencing (scRNA-seq) data have allowed us to investigate cellular heterogeneity and the kinetics of a biological process. Some studies need to understand how cells change state, and corresponding genes during the process, but it is challenging to track the cell development in scRNA-seq protocols. Therefore, a variety of statistical and computational methods have been proposed for lineage inference (or pseudotemporal ordering) to reconstruct the states of cells according to the developmental process from the measured snapshot data. Specifically, lineage refers to an ordered transition of cellular states, where individual cells represent points along. pseudotime is a one-dimensional variable representing each cell’s transcriptional progression toward the terminal state. Slingshot which is one of the methods suggested for lineage reconstruction and pseudotime inference from single-cell gene expression data. In this notebook, we will illustrate an example workflow for cell lineage and pseudotime inference using Slingshot. The notebook is inspired by Slingshot's vignette and modified to demonstrate how the tool works on BioTuring's platform.

Spatial transcriptomics (ST) technology has allowed to capture of topographical gene expression profiling of tumor tissues, but single-cell resolution is potentially lost. Identifying cell identities in ST datasets from tumors or other samples remains challenging for existing cell-type deconvolution methods. Spatial Cellular Estimator for Tumors (SpaCET) is an R package for analyzing cancer ST datasets to estimate cell lineages and intercellular interactions in the tumor microenvironment. Generally, SpaCET infers the malignant cell fraction through a gene pattern dictionary, then calibrates local cell densities and determines immune and stromal cell lineage fractions using a constrained regression model. Finally, the method can reveal putative cell-cell interactions in the tumor microenvironment. In this notebook, we will illustrate an example workflow for cell type deconvolution and interaction analysis on breast cancer ST data from 10X Visium. The notebook is inspired by SpaCET's vignettes and modified to demonstrate how the tool works on BioTuring's platform.