Package: SimBu 1.9.0
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:
SimBu_1.9.0.tar.gz
SimBu_1.9.0.zip(r-4.5)SimBu_1.9.0.zip(r-4.4)SimBu_1.9.0.zip(r-4.3)
SimBu_1.9.0.tgz(r-4.4-any)SimBu_1.9.0.tgz(r-4.3-any)
SimBu_1.9.0.tar.gz(r-4.5-noble)SimBu_1.9.0.tar.gz(r-4.4-noble)
SimBu_1.9.0.tgz(r-4.4-emscripten)SimBu_1.9.0.tgz(r-4.3-emscripten)
SimBu.pdf |SimBu.html✨
SimBu/json (API)
NEWS
| # 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-1.9.0(bioc 3.21)SimBu-1.8.0(bioc 3.20)
Last updated 23 days agofrom:38365942a5. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 31 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | NOTE | Oct 31 2024 |
| R-4.3-mac | NOTE | Oct 31 2024 |
Exports:censusdatasetdataset_h5addataset_mergedataset_seuratdataset_sfairadataset_sfaira_multiplemerge_simulationsplot_simulationsave_simulationsetup_sfairasfaira_overviewsimulate_bulk
Dependencies:abindade4apeaskpassbasiliskbasilisk.utilsBHBiobaseBiocGenericsBiocParallelbiomformatBiostringsbitopscliclustercodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydigestdir.expirydplyrfansifarverfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtableherehttrigraphIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemulttestmunsellnlmeopensslpermutephyloseqpillarpixmappkgconfigplyrpngproxyCpurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppTOMLRCurlreshape2reticulaterhdf5rhdf5filtersRhdf5librlangrprojrootS4ArraysS4VectorsscalessnowspSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsveganviridisLitewithrXVectorzlibbioc
Getting started with SimBu
Rendered fromSimBu.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2023-11-08
Started: 2022-06-01
Inputs and Outputs
Rendered fromsimulator_input_output.Rmdusingknitr::knitron Oct 31 2024.Last update: 2023-11-08
Started: 2021-12-21
Introducing mRNA bias into simulations with scaling factors
Rendered fromsimulator_scaling_factors.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2023-11-08
Started: 2021-11-29
Public Data Integration using Sfaira
Rendered fromsfaira_vignette.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2023-11-08
Started: 2022-02-06
