Package: SimBu 1.15.0

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_1.15.0.tar.gz
SimBu_1.15.0.zip(r-4.7)SimBu_1.15.0.zip(r-4.6)SimBu_1.15.0.zip(r-4.5)
SimBu_1.15.0.tgz(r-4.6-any)SimBu_1.15.0.tgz(r-4.5-any)
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SimBu_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SimBu/json (API)

# Install 'SimBu' in R:
install.packages('SimBu', repos = c('https://bioc.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

7.69 score 19 stars 1 packages 54 scripts 13 exports 92 dependencies

Last updated from:e4a5ee259a. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR192
linux-devel-x86_64NOTE788
source / vignettesOK339
linux-release-x86_64NOTE763
macos-release-arm64NOTE499
macos-oldrel-arm64NOTE659
windows-develNOTE256
windows-releaseNOTE223
windows-oldrelNOTE226
wasm-releaseOK209

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
Installation | Introduction | Getting started | Creating a dataset | Simulate pseudo bulk datasets | Results | More features | Simulate using a whitelist (and blacklist) of cell-types | References
Rendered fromSimBu.Rmdusingknitr::rmarkdown

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

Inputs and Outputs
Input | Custom data | Seurat | h5ad files | Merging datasets | Output
Rendered fromsimulator_input_output.Rmdusingknitr::knitr

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

Introducing mRNA bias into simulations with scaling factors
Using scaling factors | Pre-defined scaling factors | Dataset specific scaling factors | Reads and genes | Spike-ins | Census - estimate mRNA counts per cell | References
Rendered fromsimulator_scaling_factors.Rmdusingknitr::rmarkdown

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

Public Data Integration using Sfaira
Sfaira Integeration | Setup | Creating a dataset
Rendered fromsfaira_vignette.Rmdusingknitr::rmarkdown

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