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SimBu

Simulate Bulk RNA-seq Datasets from Single-Cell Datasets


Bioconductor version: Release (3.18)

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 "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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

Details

biocViews RNASeq, SingleCell, Software
Version 1.4.3
In Bioconductor since BioC 3.16 (R-4.2) (1.5 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)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report Build Report

Package Archives

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

Source Package SimBu_1.4.3.tar.gz
Windows Binary SimBu_1.4.3.zip
macOS Binary (x86_64) SimBu_1.4.3.tgz
macOS Binary (arm64) SimBu_1.4.0.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive