E-spatial

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.

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.

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.

PopV uses popular vote of a variety of cell-type transfer tools to classify cell-types in a query dataset based on a test dataset. Using this variety of algorithms, they compute the agreement between those algorithms and use this agreement to predict which cell-types have a high likelihood of the same cell-types observed in the reference.