Package: scTensor 2.23.0

Specification change of LRBase and scTensor from BioC 3.14 (Nov. 2021) | Introduction | About Cell-Cell Interaction (CCI) databases | LRBase and scTensor framework | Usage | LRBase objects (ligand-receptor database for 134 organisms) | Data retrieval from AnnotationHub | columns, keytypes, keys, and select | Other functions | scTensor (CCI-tensor construction, decomposition, and HTML reporting) | Creating a SingleCellExperiment object | Parameter setting: cellCellSetting | CCI-tensor construction and decomposition: cellCellDecomp | HTML Report: cellCellReport | Session Information

Introduction | Step.1: Create a gene-level expression matrix | Case I: Gene-level quantification | Case II: Transcript-level quantification | Case III: UMI-count | Step.2: Convert the row names of a matrix as NCBI Gene ID (ENTREZID) | Case I: Ensembl Gene ID to NCBI Gene ID | Case II: Gene Symbol to NCBI Gene ID | Step.3: Normalize the count matrix | Session information

Summary of the output objects of scTensor | Execution of scTensor with the different options | Session information

Introduction | Interpretation of "1. About scTensor Algorithm" | Interpretation of "2. Global statistics and plots" | Interpretation of "3. Ligand-Cell Patterns" | Interpretation of "4. Receptor-Cell Patterns" | Interpretation of "5. CCI-wise Hypergraph" | Interpretation of "6. Gene-wise Hypergraph" | Interpretation of "7. (Ligand-Cell, Receptor-Cell, LR-pair) Patterns" | Session information

Introduction | Session information