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.
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")
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.
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