SimBu
Simulate Bulk RNA-seq Datasets from Single-Cell Datasets
Bioconductor version: Release (3.19)
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("SimBu")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | RNASeq, SingleCell, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 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 | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SimBu_1.6.0.tar.gz |
| Windows Binary (x86_64) | SimBu_1.6.0.zip |
| macOS Binary (x86_64) | SimBu_1.6.0.tgz |
| macOS Binary (arm64) | SimBu_1.6.0.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 3.19 | Source Archive |