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Semi-parametric simulation tool for bulk and single-cell RNA sequencing data

Bioconductor version: Release (3.19)

SPsimSeq uses a specially designed exponential family for density estimation to constructs the distribution of gene expression levels from a given real RNA sequencing data (single-cell or bulk), and subsequently simulates a new dataset from the estimated marginal distributions using Gaussian-copulas to retain the dependence between genes. It allows simulation of multiple groups and batches with any required sample size and library size.

Author: Alemu Takele Assefa [aut], Olivier Thas [ths], Joris Meys [cre], Stijn Hawinkel [aut]

Maintainer: Joris Meys <Joris.Meys at>

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


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:

Manual for the SPsimSeq package: semi-parametric simulation for bulk and single cell RNA-seq data HTML R Script
Reference Manual PDF


biocViews DNASeq, GeneExpression, RNASeq, Sequencing, SingleCell, Software
Version 1.14.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-2
Depends R (>= 4.0)
Imports stats, methods, SingleCellExperiment, fitdistrplus, graphics, edgeR, Hmisc, WGCNA, limma, mvtnorm, phyloseq, utils
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Suggests knitr, rmarkdown, LSD, testthat, BiocStyle
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SPsimSeq_1.14.0.tar.gz
Windows Binary
macOS Binary (x86_64) SPsimSeq_1.14.0.tgz
macOS Binary (arm64) SPsimSeq_1.14.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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