Preprocessing: pp

Utilities used by scBIOT to prepare AnnData objects before OT alignment

annotate_gene_activity	Build a gene-activity AnnData by assigning ATAC peaks to genes.
remove_promoter_proximal_peaks	Remove peaks that overlap promoter windows defined from a GTF.
add_iterative_lsi	Convenience wrapper that runs iterative LSI.
create_gene_activity	Build gene-activity (GA) from ATAC peaks and harmonize GA gene names to RNA.
coembed_pca	Shared PCA coembedding (reference-fitted PCA, query projection) and optional per-cluster outlier flagging.