Package: SimBu 1.7.0

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_1.7.0.tar.gz
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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-1.7.0(bioc 3.20)SimBu-1.6.0(bioc 3.19)

bioconductor-package

13 exports 1.08 score 107 dependencies

Last updated 2 months agofrom:b412ad3351

Exports:census dataset dataset_h5ad dataset_merge dataset_seurat dataset_sfaira dataset_sfaira_multiple merge_simulations plot_simulation save_simulation setup_sfaira sfaira_overview simulate_bulk

Dependencies:abind ade4 ape askpass basilisk basilisk.utils BH Biobase BiocGenerics BiocParallel biomformat Biostrings bitops cli cluster codetools colorspace cpp11 crayon curl data.table DelayedArray digest dir.expiry dplyr fansi farver filelock foreach formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable here httr igraph IRanges isoband iterators jsonlite labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime multtest munsell nlme openssl permute phyloseq pillar pixmap pkgconfig plyr png proxyC purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppTOML RCurl reshape2 reticulate rhdf5 rhdf5filters Rhdf5lib rlang rprojroot S4Arrays S4Vectors scales snow sp SparseArray sparseMatrixStats stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect UCSC.utils utf8 vctrs vegan viridisLite withr XVector zlibbioc

Getting started with SimBu

Alexander Dietrich

Rendered fromSimBu.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-11-08
Started: 2022-06-01

Inputs and Outputs

Alexander Dietrich

Rendered fromsimulator_input_output.Rmdusingknitr::knitron Jun 30 2024.

Last update: 2023-11-08
Started: 2021-12-21

Introducing mRNA bias into simulations with scaling factors

Alexander Dietrich

Rendered fromsimulator_scaling_factors.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-11-08
Started: 2021-11-29

Public Data Integration using Sfaira

Alexander Dietrich

Rendered fromsfaira_vignette.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-11-08
Started: 2022-02-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Applies the Census count transformation on a count matrix	census
Build SummarizedExperiment using local annotation and count matrix R objects	dataset
Build SummarizedExperiment using a h5ad file for the counts	dataset_h5ad
Merge multiple SummarizedExperiment datasets into one	dataset_merge
Build SummarizedExperiment using a Seurat object	dataset_seurat
Build SummarizedExperiment using a single sfaira entry ID	dataset_sfaira
Build SummarizedExperiment using multiple sfaira entries	dataset_sfaira_multiple
Combine multiple simulations into one result	merge_simulations
Plot the cell-type fractions in your simulated dataset	plot_simulation
Save the expression matrix of a simulated pseudo-bulk dataset to a file	save_simulation
setup the sfaira package	setup_sfaira
Gives an overview of the possible datasets you can use from the sfaira database	sfaira_overview
SimBu: Bias-aware simulation of bulk RNA-seq data with variable cell type composition	SimBu
Simulate whole pseudo-bulk RNAseq dataset	simulate_bulk

Package: SimBu 1.7.0

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

Getting started with SimBu

Inputs and Outputs

Introducing mRNA bias into simulations with scaling factors

Public Data Integration using Sfaira

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)