DOI: 10.18129/B9.bioc.SimBu    

This is the development version of SimBu; for the stable release version, see SimBu.

Simulate Bulk RNA-seq Datasets from Single-Cell Datasets

Bioconductor version: Development (3.17)

SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions. You can either use your own single-cell study for the simulation or the sfaira database. Different pre-defined simulation scenarios exist, as are options to run custom simulations. Additionally, expression values can be adapted by adding an mRNA bias, which produces more biologically relevant simulations.

Author: Alexander Dietrich [aut, cre]

Maintainer: Alexander Dietrich <alex.dietrich at>

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


To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel


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HTML R Script Getting started
HTML R Script Inputs and Outputs
HTML R Script Introducing mRNA bias into simulations with scaling factors
HTML R Script Public Data Integration using Sfaira
PDF   Reference Manual


biocViews RNASeq, SingleCell, Software
Version 1.1.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License GPL-3 + file LICENSE
Imports basilisk, BiocParallel, data.table, dplyr, ggplot2, tools, Matrix (>= 1.3.3), methods, phyloseq, proxyC, RColorBrewer, RCurl, reticulate, sparseMatrixStats, SummarizedExperiment, tidyr
Suggests curl, knitr, matrixStats, rmarkdown, Seurat, testthat (>= 3.0.0)
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