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omnideconv / SimBu

Simulate pseudo-bulk RNAseq samples from scRNAseq expression data
http://omnideconv.org/SimBu/
GNU General Public License v3.0
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SimBu

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The goal of SimBu is to simulate pseudo-bulk RNAseq datasets with variable cell-type fractions baed on public or private single-cell RNAseq datasets.

Installation

To install the developmental version of the package, run:

install.packages("devtools")
devtools::install_github("omnideconv/SimBu")

To install from Bioconductor:

if (!require("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}

BiocManager::install("SimBu")

Usage

Create a dataset-object with local data and simulate a pseudo-bulk dataset

library(SimBu)
# use local data to build dataset
dataset <- dataset(annotation = annotation_dataframe, count_matrix = expression_matrix, name = "test_dataset")
simulation <- simulate_bulk(data = dataset, scenario = "random", scaling_factor = "NONE")

For more detailed usage instructions, check out Getting started.

You can find more information on the simulation setup and mRNA bias in our SimBu publication.