SimBu

Simulate Bulk RNA-seq Datasets from Single-Cell Datasets

Bioconductor version: Release (3.17)

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	1.2.0
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
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
Linking To
Suggests	curl, knitr, matrixStats, rmarkdown, Seurat, testthat (>= 3.0.0)
System Requirements
Enhances
URL	https://github.com/omnideconv/SimBu
Bug Reports	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_1.2.0.tar.gz
Windows Binary	SimBu_1.2.0.zip
macOS Binary (x86_64)	SimBu_1.2.0.tgz
macOS Binary (arm64)	SimBu_1.2.0.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