rescueSim: Repeated measures single cell RNA-sequencing data simulation

rescueSim is an R package for simulating repeated measures (paired/longitudinal) single-cell RNA-sequencing (scRNA-seq) data.
It is designed to support power analysis, benchmarking, and method development for studies involving complex scRNA-seq designs.

Explore rescueSim

• Introduction to rescueSim
• Power analysis with rescueSim
• Function Documentation

Getting started

Install dependencies

## CRAN packages
install.packages(c("checkmate", "dplyr", "gtools", "Matrix", "lme4"))

## Bioconductor packages
if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}

BiocManager::install(c("scater", "edgeR", "scran", "scater", "scuttle", "SingleCellExperiment", "MAST"))

Install rescueSim from GitHub

Note: The package vignettes are available on the package website. If you’d prefer to build the vignettes locally during installation, you can set build_vignettes = TRUE, though this may take longer.

if (!requireNamespace("devtools", quietly = TRUE)) {
  install.packages("devtools")
}
devtools::install_github("https://github.com/ewynn610/rescueSim",  build_vignettes = FALSE)