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Bioconductor - 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

Bioconductor version: Development (3.22)

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 "4.5") 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")
Details biocViews RNASeq, SingleCell, Software Version 1.11.0 In Bioconductor since BioC 3.16 (R-4.2) (2.5 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 Package Archives

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

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