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SimBu (development version)

SimBu

This is the development version of SimBu; for the stable release version, see SimBu.

Simulate Bulk RNA-seq Datasets from Single-Cell Datasets

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DOI: 10.18129/B9.bioc.SimBu

Bioconductor version: Development (3.23)

SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions. You can either use your own single-cell study for the simulation or the sfaira database. Different pre-defined simulation scenarios exist, as are options to run custom simulations. Additionally, expression values can be adapted by adding an mRNA bias, which produces more biologically relevant simulations.

Author: Alexander Dietrich [aut, cre]

Maintainer: Alexander Dietrich <alex.dietrich at tum.de>

Citation (from within R, enter citation("SimBu")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("SimBu")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SimBu")

Getting started HTML R Script

Inputs and Outputs HTML R Script

Introducing mRNA bias into simulations with scaling factors HTML R Script

Public Data Integration using Sfaira HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews RNASeq, SingleCell, Software

Version 1.13.0

In Bioconductor since BioC 3.16 (R-4.2) (3 years)

License GPL-3 + file LICENSE

Depends

Imports basilisk, BiocParallel, data.table, dplyr, ggplot2, tools, Matrix (>= 1.3.3), methods, phyloseq, proxyC, RColorBrewer, RCurl, reticulate, sparseMatrixStats, SummarizedExperiment, tidyr

System Requirements

URL https://github.com/omnideconv/SimBu

Bug Reports https://github.com/omnideconv/SimBu/issues

See More

Suggests curl, knitr, matrixStats, rmarkdown, Seurat (>= 5.0.0), SeuratObject (>= 5.0.0), testthat (>= 3.0.0)

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SimBu_1.13.0.tar.gz

Windows Binary (x86_64) SimBu_1.13.0.zip

macOS Binary (x86_64) SimBu_1.13.0.tgz

macOS Binary (arm64) SimBu_1.13.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/SimBu

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SimBu

Bioc Package Browser https://code.bioconductor.org/browse/SimBu/

Package Short Url https://bioconductor.org/packages/SimBu/

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