Package index • SCUBA

Data exploration

meta_varnames(): Summarize object metadata

unique_values(): Summarize values in a metadata variable

Data access

fetch_data(): Fetch feature expression data, reduction coordinates, or metadata from single-cell objects

fetch_metadata(): Fetch metadata from single-cell objects

fetch_reduction(): Fetch reduction coordinates from single-cell objects

Utility functions

reduction_dimnames(): From names of reduction keys for fetch_data

fetch_cells(): Return cell IDs for a subset based on metadata

all_keys(): Get keys for all assays/reductions in an object

features_in_assay(): Get names of all features in an assay/experiment/modality

default_layer(): Return the default layer

default_reduction(): Get default reduction from object

get_all_cells(): Plotting utility function to return all cell IDs

n_unique(): Number of unique values in a metadata variable

Datasets

AML_Seurat: Reference dataset used for testing and demonstration (Seurat)

AML_SCE(): Reference dataset used for testing and demonstration (SingleCellExperiment)

AML_h5ad() AML_h5ad_backed(): Reference dataset used for testing and demonstration (anndata)