Function reference • Simba4Bioc

All functions
`basic_preproc()`	Transform an AnnData input to one that has had gene filtering, normalization, log transformation, low-variance gene exclusion, and discretization applied.
`build_and_train_pbg()`	build and train SIMBA PBG graph
`compare_entities()`	use the compare_entities method to assess 'closeness' of embedded elements
`flatten_json()`	Helper function to recursively flatten nested lists produced by Chat-GPT 3
`get_10x3kpbmc_path()`	retrieve path to 10x 3k PBMC h5ad (compressed)
`get_3k_cell_emb()`	retrieve path to the 3k PBMC cell embedding in AnnData format
`get_3k_gene_emb()`	retrieve path to the 3k PBMC gene embedding in AnnData format
`get_emb_h5()`	retrieve and HDF5 representation of an embedding produced by pbg in simba
`get_paul15_path()`	retrieve path to Paul 2015 (Cell 163:7, 1663) AnnData instance
`ingest_training_stats()`	get pbg_metrics data frames
`propagate_label()`	propagation -- updates a post-train cell embedding, in which embedding "rows" corresponding to cells have been reordered, adding a column to the `obs` component
`scanpy_ref()`	hand scanpy from specified basilisk environment
`simba_barcode_data()`	'barcode' data for figure 2d of original simba paper
`simba_ref()`	hand sfaira from specified basilisk environment

Reference