Scaffold: data-generation simulation of single-cell RNA-seq data

Scaffold is an R package for generating scRNA-seq data by statistically modeling each step of the experimental data generation process. Scaffold is able to simulate non-UMI, UMI, and 10X data.

Installation

Scaffold can be installed from Github:

if (!requireNamespace("devtools", quietly=TRUE))
    install.packages("devtools")
devtools::install_github("rhondabacher/scaffold")

Vignette

Details and examples on how to use the Scaffold R package are located:

• Scaffold Vignette

Citation

Additional details on the Scaffold simulation scheme are available in the manuscript:

Rhonda Bacher, Li-Fang Chu, Cara Argus, Jennifer M Bolin, Parker Knight, James A Thomson, Ron Stewart, Christina Kendziorski, Enhancing biological signals and detection rates in single-cell RNA-seq experiments with cDNA library equalization, Nucleic Acids Research, Volume 50, Issue 2, 25 January 2022, Page e12, https://doi.org/10.1093/nar/gkab1071.

Contact/Maintainer

• Rhonda Bacher ([email protected])
  Department of Biostatistics, University of Florida