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Simulation of Multi-Modality Single Cell Data Guided By Gene Regulatory Networks and Cell-Cell Interactions

Bioconductor version: Release (3.19)

scMultiSim simulates paired single cell RNA-seq, single cell ATAC-seq and RNA velocity data, while incorporating mechanisms of gene regulatory networks, chromatin accessibility and cell-cell interactions. It allows users to tune various parameters controlling the amount of each biological factor, variation of gene-expression levels, the influence of chromatin accessibility on RNA sequence data, and so on. It can be used to benchmark various computational methods for single cell multi-omics data, and to assist in experimental design of wet-lab experiments.

Author: Hechen i [aut, cre] , Xiuwei Zhang [aut], Michael Squires [aut]

Maintainer: Hechen i <hli691 at>

Citation (from within R, enter citation("scMultiSim")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

scMultiSim Basics HTML R Script
spatialCCI.html HTML R Script
Reference Manual PDF


biocViews ExperimentalDesign, GeneExpression, Sequencing, SingleCell, Software, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License Artistic-2.0
Depends R (>= 4.4.0)
Imports foreach, rlang, dplyr, ggplot2, Rtsne, ape, MASS, matrixStats, phytools, KernelKnn, gplots, zeallot, crayon, assertthat, igraph, methods, grDevices, graphics, stats, utils, markdown, SummarizedExperiment
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Suggests knitr, rmarkdown, roxygen2, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package scMultiSim_1.0.0.tar.gz
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macOS Binary (x86_64) scMultiSim_1.0.0.tgz
macOS Binary (arm64) scMultiSim_1.0.0.tgz
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Source Repository (Developer Access) git clone
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