E-spatial

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.

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.

Classification of tumor and normal cells in the tumor microenvironment from scRNA-seq data is an ongoing challenge in human cancer study. Copy number karyotyping of aneuploid tumors (***copyKAT***) (Gao, Ruli, et al., 2021) is a method proposed for identifying copy number variations in single-cell transcriptomics data. It is used to predict aneuploid tumor cells and delineate the clonal substructure of different subpopulations that coexist within the tumor mass. In this notebook, we will illustrate a basic workflow of CopyKAT based on the tutorial provided on CopyKAT's repository. We will use a dataset of triple negative cancer tumors sequenced by 10X Chromium 3'-scRNAseq (GSM4476486) as an example. The dataset contains 20,990 features across 1,097 cells. We have modified the notebook to demonstrate how the tool works on BioTuring's platform.

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.