Function reference • SimBu

Dataset generation

Methods linked to generating the internal dataset object

dataset(): Build SummarizedExperiment using local annotation and count matrix R objects

dataset_h5ad(): Build SummarizedExperiment using a h5ad file for the counts

dataset_seurat(): Build SummarizedExperiment using a Seurat object

dataset_sfaira(): Build SummarizedExperiment using a single sfaira entry ID

dataset_sfaira_multiple(): Build SummarizedExperiment using multiple sfaira entries

dataset_merge(): Merge multiple SummarizedExperiment datasets into one

Simulation

Methods linked to simulating pseudo-bulk datasets

simulate_bulk(): Simulate whole pseudo-bulk RNAseq dataset

merge_simulations(): Combine multiple simulations into one result

save_simulation(): Save the expression matrix of a simulated pseudo-bulk dataset to a file

Other

Different methods

sfaira_overview(): Gives an overview of the possible datasets you can use from the sfaira database

plot_simulation(): Plot the cell-type fractions in your simulated dataset

setup_sfaira(): setup the sfaira package