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 this package, use the following command:
install.packages("devtools")
devtools::install_github("omnideconv/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 preprint.