Package: scPAS 1.0.4

Introduction | Biological Question | Clinical Context | Setup | Simulated Immunotherapy Data | Single-Cell Data: Pre-treatment Tumor Biopsies | Bulk Data: Pre-treatment with Response Annotation | Visualize Response Distribution | Run scPAS with Binomial Family | Visualize Results | UMAP Overview | Cell Type Response Association | Detailed Violin Plot | Stacked Bar Plot | Biological Interpretation | Responder-Associated Populations (scPAS+) | Non-Responder-Associated Populations (scPAS-) | Predictive Signature | Extract Response Signature | Signature Visualization | Publication Figure | Clinical Application | Predict Response for New Patients | Key Takeaways | Session Information

Introduction | Biological Question | Analysis Overview | Setup | Simulated Cancer Data | Single-Cell Data: Tumor Microenvironment | Bulk Data: TCGA-like Cohort with Survival | Visualize Survival Data | Run scPAS with Cox Regression | Visualize Results | UMAP Overview | Cell Type Enrichment | Violin Plot by Cell Type | Biological Interpretation | Key Findings | Publication Figure | Model Application to New Data | Key Takeaways | Session Information

Introduction | Installation | Apply scPAS with Cox regression | Load data | Prepare the scRNA-seq data | Prepare the bulk data and phenotype | Run scPAS without imputation | Run scPAS with imputation | Apply the trained model to independent bulk data | Apply the trained model to spatial transcriptomics data | Information about the current R session

Overview | Mathematical Framework | Problem Formulation | Network-Regularized Sparse Regression | Loss Functions by Phenotype Type | Gaussian Family (Continuous) | Binomial Family (Binary) | Cox Family (Survival) | Gene Network Construction | Shared Nearest Neighbor (SNN) Network | Risk Score Calculation | Per-Cell Risk Score | Normalized Risk Score | Statistical Significance Testing | Permutation Test | FDR Correction | Cell Classification | Implementation Details | Sparse Matrix Operations | Parallel Computing | References | Session Information

Introduction | Key Features | Package Installation | Quick Example | Load Required Packages | Simulate Example Data | Preprocess Single-Cell Data | Run scPAS Analysis | Examine Results | Basic Visualization | Output Structure | Three Phenotype Types | 1. Continuous Phenotype (Gaussian) | 2. Binary Phenotype (Binomial) | 3. Survival Phenotype (Cox) | Next Steps | Session Information

Introduction | Setup and Simulated Data | Create Simulated scPAS Result | Basic UMAP Plots | Cell Type Overview | Risk Score Visualization | Cell Classification | Combined Multi-Panel Plot | Cell Type Enrichment Analysis | Proportion Bar Plot | Enrichment Heatmap | Volcano-Style Plot | Violin Plots | Risk Score by Cell Type | Split Violin by Classification | Box Plots with Statistical Tests | Density Plots | Pie Chart Summary | Publication-Ready Figure | Saving Plots | Session Information