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https://github.com/bioconductor-source/simbu

https://github.com/bioconductor-source/simbu

Science Score: 26.0%

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Repository

Basic Info
  • Host: GitHub
  • Owner: bioconductor-source
  • License: gpl-3.0
  • Language: R
  • Default Branch: devel
  • Size: 11.7 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog License

README.Rmd 

---
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).

Owner

  • Name: (WIP DEV) Bioconductor Packages
  • Login: bioconductor-source
  • Kind: organization
  • Email: maintainer@bioconductor.org

Source code for packages accepted into Bioconductor

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Dependencies

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.github/workflows/test.yml actions
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  • r-lib/actions/setup-pandoc v2 composite
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DESCRIPTION cran
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