Yue Lyu

This paper introduces SuperSurv , a user-friendly R package for building, evaluating, and interpreting ensemble models for right-censored survival data. Although many survival modeling methods are available, existing tools are often model-specific and lack a unified platform for systematically integrating, comparing, and ensembling heterogeneous learners. SuperSurv addresses this gap by providing a unified interface for diverse survival learners, including models that return full survival curves as well as methods that produce only risk scores. All learner outputs are mapped to calibrated survival probability curves on a common evaluation time grid, enabling direct comparison and ensemble construction across heterogeneous model classes. SuperSurv implements stacking of survival models using inverse-probability-of-censoring weighted (IPCW) Brier risk to estimate ensemble weights in the presence of right censoring. The framework integrates hyperparameter tuning, time-dependent benchmarking metrics, and visualization tools for survival model evaluation. In addition, the package provides post-hoc interpretability utilities based on SHAP(SHapley Additive exPlanations) values and supports covariate-adjusted restricted mean survival time (RMST) contrasts through g-computation. By bridging the gap between theoretical rigor and clinical application, SuperSurv offers researchers a comprehensive ecosystem for modern survival analysis. The SuperSurv package is open-source and available on CRAN at https://CRAN.R-project.org/package=SuperSurv and on GitHub at https://github.com/yuelyu21/SuperSurv . An empirical example using the METABRIC breast cancer dataset demonstrates a complete workflow from model training and benchmarking to explainability and clinically interpretable survival contrasts.

Motivation: The growing number of single-cell RNA-seq (scRNA-seq) studies highlights the potential benefits of integrating multiple datasets, such as augmenting sample sizes and enhancing analytical robustness. Inherent diversity and batch discrepancies within samples or across studies continue to pose significant challenges for computational analyses. Questions persist in practice, lacking definitive answers: Should we use a specific integration method or opt for simply merging the datasets during joint analysis? Among all the existing data integration methods, which one is more suitable in specific scenarios? Result: To fill the gap, we introduce SCIntRuler, a novel statistical metric for guiding the integration of multiple scRNA-seq datasets. SCIntRuler helps researchers make informed decisions regarding the necessity of data integration and the selection of an appropriate integration method. Our simulations and real data applications demonstrate that SCIntRuler streamlines decision-making processes and facilitates the analysis of diverse scRNA-seq datasets under varying contexts, thereby alleviating the complexities associated with the integration of heterogeneous scRNA-seq datasets. Availability and implementation: The implementation of our method is available on CRAN as an open-source R package with a user-friendly manual available: https://cloud.r-project.org/web/packages/SCIntRuler/index.html

Motivation: Spatial transcriptomics has greatly contributed to our understanding of spatial and intra-sample heterogeneity, which could be crucial for deciphering the molecular basis of human diseases. Intra-tumor heterogeneity, e.g. may be associated with cancer treatment responses. However, the lack of computational tools for exploiting cross-regional information and the limited spatial resolution of current technologies present major obstacles to elucidating tissue heterogeneity. Results: To address these challenges, we introduce RegionalST, an efficient computational method that enables users to quantify cell type mixture and interactions, identify sub-regions of interest, and perform cross-region cell type-specific differential analysis for the first time. Our simulations and real data applications demonstrate that RegionalST is an efficient tool for visualizing and analyzing diverse spatial transcriptomics data, thereby enabling accurate and flexible exploration of tissue heterogeneity. Overall, RegionalST provides a one-stop destination for researchers seeking to delve deeper into the intricacies of spatial transcriptomics data. Availability and implementation: The implementation of our method is available as an open-source R/Bioconductor package with a user-friendly manual available at https://bioconductor.org/packages/release/bioc/html/RegionalST.html.