Package: SimBu 1.14.0

Alexander Dietrich

SimBu: Simulate Bulk RNA-seq Datasets from Single-Cell Datasets

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.

Authors:Alexander Dietrich [aut, cre]

SimBu_1.14.0.tar.gz
SimBu_1.14.0.zip(r-4.7)SimBu_1.14.0.zip(r-4.6)SimBu_1.14.0.zip(r-4.5)
SimBu_1.14.0.tgz(r-4.6-any)SimBu_1.14.0.tgz(r-4.5-any)
SimBu_1.14.0.tar.gz(r-4.7-any)SimBu_1.14.0.tar.gz(r-4.6-any)
SimBu_1.14.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SimBu/json (API)
NEWS

# Install 'SimBu' in R:
install.packages('SimBu', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/omnideconv/simbu/issues

On BioConductor:SimBu-1.15.0(bioc 3.24)SimBu-1.14.0(bioc 3.23)

softwarernaseqsinglecell

7.65 score 19 stars 1 packages 49 scripts 316 downloads 13 exports 92 dependencies

Last updated from:0e37940b95 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR177
linux-devel-x86_64NOTE799
source / vignettesOK280
linux-release-x86_64NOTE769
macos-release-arm64NOTE712
macos-oldrel-arm64NOTE570
windows-develNOTE276
windows-releaseNOTE223
windows-oldrelNOTE218
wasm-releaseOK178

Exports:censusdatasetdataset_h5addataset_mergedataset_seuratdataset_sfairadataset_sfaira_multiplemerge_simulationsplot_simulationsave_simulationsetup_sfairasfaira_overviewsimulate_bulk

Dependencies:abindade4apebasiliskBHBiobaseBiocGenericsBiocParallelbiomformatBiostringsbitopscliclustercodetoolscpp11crayondata.tableDelayedArraydigestdir.expirydplyrfarverfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehereigraphIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmulttestnlmepermutephyloseqpillarpixmappkgconfigplyrpngproxyCpurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppTOMLRCurlreshape2reticulaterlangrprojrootS4ArraysS4VectorsS7scalesSeqinfosnowspSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsurvivaltibbletidyrtidyselectutf8vctrsveganviridisLitewithrXVector

Getting started with SimBu

Alexander Dietrich

Rendered fromSimBu.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-03-28
Started: 2022-06-01

Inputs and Outputs

Alexander Dietrich

Rendered fromsimulator_input_output.Rmdusingknitr::knitron May 30 2026.

Last update: 2025-03-28
Started: 2021-12-21

Introducing mRNA bias into simulations with scaling factors

Alexander Dietrich

Rendered fromsimulator_scaling_factors.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-03-28
Started: 2021-11-29

Public Data Integration using Sfaira

Alexander Dietrich

Rendered fromsfaira_vignette.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-03-28
Started: 2022-02-06