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README.md
<!-- README.md is generated from README.Rmd. Please edit that file --> # SimBu <!-- badges: start --> [![tests](https://github.com/omnideconv/SimBu/actions/workflows/test.yml/badge.svg)](https://github.com/omnideconv/SimBu/actions/workflows/test.yml) [![license](https://img.shields.io/badge/license-LGPLv3-blue.svg)](https://github.com/omnideconv/SimBu/blob/master/LICENSE.md) [![docs](https://img.shields.io/badge/docs-pkgdown-blue.svg)](https://omnideconv.github.io/SimBu) [![Codecov test coverage](https://codecov.io/gh/omnideconv/SimBu/branch/master/graph/badge.svg)](https://app.codecov.io/gh/omnideconv/SimBu?branch=master) <!-- badges: end --> 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: ``` r install.packages("devtools") devtools::install_github("omnideconv/SimBu") ``` To install from Bioconductor: ``` r 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 ``` r 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](http://omnideconv.org/SimBu/articles/simulator_documentation.html). You can find more information on the simulation setup and mRNA bias in our [SimBu publication](https://doi.org/10.1093/bioinformatics/btac499).