ArticleBioinformatics (Oxford, England)2025
Simulating paired and longitudinal single-cell RNA sequencing data with rescueSim.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
5 citing papers in PubMed.
- Clonal Metamorphosis: Deconstructing MPN Evolution with Single-Cell and Spatial Multi-Omics.Clinical and experimental medicine · 2026Review
- scLASER: a robust framework for simulating and detecting time-dependent single-cell dynamics in longitudinal studies.bioRxiv : the preprint server for biology · 2026Article
- scDesignPop generates realistic population-scale single-cell RNA-seq for power analysis, benchmarking, and privacy protection.bioRxiv : the preprint server for biology · 2026Article
- Longitudinal omics data analysis: approaches and applications.Computational and structural biotechnology journal · 2026Review
- CRISPR and Artificial Intelligence in Neuroregeneration: Closed-Loop Strategies for Precision Medicine, Spinal Cord Repair, and Adaptive Neuro-Oncology.International journal of molecular sciences · 2025Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
motivationAs single-cell RNA-sequencing (scRNA-seq) becomes more widely used in transcriptomic research, complex experimental designs, such as paired or longitudinal studies, become increasingly feasible. Paired/longitudinal scRNA-seq enables the study of transcriptomic changes over time within specific cell types, yet guidance on analytical approaches and resources for study planning, such as power analysis, remains limited. Data simulation is a valuable tool for evaluating analysis method performance and informing study design decisions, including sample size selection. Currently, most scRNA-seq simulation methods simulate cells for a single sample, thus ignoring the between-sample and between-subject variability inherent to paired/longitudinal scRNA-seq data.
resultsHere, we introduce rescueSim (REpeated measures Single Cell RNA-seqUEncing data SIMulation), a novel method that simulates paired/longitudinal scRNA-seq data using a gamma-Poisson framework and incorporates additional variability between samples and subjects. We demonstrate our method's ability to reproduce important data properties and demonstrate its application in study planning. AVAILABILITY AND IMPLEMENTATION: rescueSim is implemented as an R package and is available at https://github.com/ewynn610/rescueSim.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.