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