SimBu
This is the released version of SimBu; for the devel version, see SimBu.
Simulate Bulk RNA-seq Datasets from Single-Cell Datasets
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.14.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 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_1.14.0.tar.gz |
| Windows Binary (x86_64) | SimBu_1.14.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | SimBu_1.14.0.tgz |
| macOS Binary (sonoma-arm64) | SimBu_1.14.0.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 |