Man pages for omnideconv/SimBu
Simulate Bulk RNA-seq Datasets from Single-Cell Datasets
| calc_scaling_vector | Calculate scaling factor for a dataset |
| census | Applies the Census count transformation on a count matrix |
| census_monocle | Census calculation as implemented in monocle |
| check_annotation | check for correct column names in annotation file and replace... |
| check_if_tpm | Checks, if a matrix is TPM-like (columns sum up to 1e6) |
| compare_matrix_with_annotation | Check if annotation and matrix have same cells |
| dataset | Build SummarizedExperiment using local annotation and count... |
| 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 |
| dmode | use gaussian kernel to calculate the mode of transcript... |
| download_sfaira | download a specific dataset from sfaira by an ID |
| download_sfaira_multiple | download multiple datasets from sfaira using filters for... |
| filter_matrix | filter one (or two) expression matrix by genes |
| generate_summarized_experiment | Generate SummarizedExperiment using multiple parameters |
| h5ad_to_adata | Use basilisk environment to read h5ad file and access anndata... |
| merge_scaling_factor | Create scaling vector from custom or pre-defined scaling... |
| 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... |
| setup_sfaira | setup the sfaira package |
| sfaira_overview | Gives an overview of the possible datasets you can use from... |
| SimBu | SimBu: Bias-aware simulation of bulk RNA-seq data with... |
| simulate_bulk | Simulate whole pseudo-bulk RNAseq dataset |
| simulate_sample | simulate single pseudo-bulk sample |
