Package: xCell2 1.5.0

Introduction to xCell 2.0 and Key Features | Custom Reference Training | Ontological Integration | Spillover Correction | Installation | Creating a Custom Reference with xCell2Train | Why Create a Custom Reference? | Preparing the Input Data | 1. Reference Gene Expression Matrix | 2. Labels Data Frame | Using SummarizedExperiment or SingleCellExperiment Objects | Example: preparing the input data | Assigning Cell Type Ontology (optional but recommended) | When to Skip Ontology Assignment | Assigning Ontologies | Example: assigning cell type ontology | Example: checking lineage relationships | Generating the xCell2 Reference Object | Key Parameters of xCell2Train | Example: generating xCell2 reference object | Sharing Your Custom xCell2 Reference Object | Next Steps | Using Pre-trained xCell2 References | Available Pre-trained References | Accessing Pre-trained References | Choosing the Right Reference | Calculating Cell Type Enrichment with xCell2Analysis | Preparing the Input Data | Key Parameters of xCell2Analysis | Calculating Cell Type Enrichment | Understanding Enrichment Scores | Advanced Analysis with xCell2 Results | Normalizing Enrichment Scores by Tumor Purity | Comparing Cellular Enrichment Across Conditions | Correlating Enrichment Scores with Clinical or Molecular Features | Clustering and Dimension Reduction | Using Enrichment Scores as Features for Predictive Modeling | Parallelization in xCell2 | Citing xCell2 | Referece | R Session Info