https://github.com/omnideconv/SimBu

Simulate pseudo-bulk RNAseq samples from scRNAseq expression data
https://github.com/omnideconv/SimBu

Last synced: 17 days ago
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Simulate pseudo-bulk RNAseq samples from scRNAseq expression data

• Host: GitHub
• URL: https://github.com/omnideconv/SimBu
• Owner: omnideconv
• License: gpl-3.0
• Created: 2021-05-14T14:43:10.000Z (about 3 years ago)
• Default Branch: devel
• Last Pushed: 2024-05-06T17:21:01.000Z (about 2 months ago)
• Last Synced: 2024-06-07T11:22:58.536Z (25 days ago)
• Language: R
• Homepage: http://omnideconv.org/SimBu/
• Size: 18.6 MB
• Stars: 12
• Watchers: 5
• Forks: 1
• Open Issues: 7
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE

Lists

• awesome-deconvolution - SimBu - bulk RNAseq datasets with variable cell-type fractions baed on public or private single-cell RNAseq datasets ([Dietrich et al 2022](https://academic.oup.com/bioinformatics/article/38/Supplement_2/ii141/6702009); tags: pseudobulk; single-cell; rna-seq; simulation; bias; cell_size; scale_factor; transcriptomics; bulk). (Methods)

README

        
---

output: github_document

---

```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```

# SimBu

[![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)

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, eval=FALSE}

install.packages("devtools")

devtools::install_github("omnideconv/SimBu")

```

To install from Bioconductor:

```{r, eval=FALSE}

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 example, eval=FALSE}

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).