SimBu

DOI: 10.18129/B9.bioc.SimBu  

Simulate Bulk RNA-seq Datasets from Single-Cell Datasets

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	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
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	RNASeq, SingleCell, Software
Version	1.0.2
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
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
LinkingTo
Suggests	curl, knitr, matrixStats, rmarkdown, Seurat, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/omnideconv/SimBu
BugReports	https://github.com/omnideconv/SimBu/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SimBu_1.0.2.tar.gz
Windows Binary	SimBu_1.0.2.zip
macOS Binary (x86_64)	SimBu_1.0.2.tgz
macOS Binary (arm64)	SimBu_1.0.2.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 3.16	Source Archive