insitucnv.tl.cnv

Functions

assign_cnv_status(adata, cluster_key[, ...])	Annotate CNV clusters as tumor/normal from explicit cluster choices.
assign_cnv_subclones(adata, cluster_key, ...)	Label explicitly selected tumor CNV clusters as separate clone groups.
cluster_cnv_resolutions(adata, resolutions)	Cluster CNV profiles at one or more Leiden resolutions.
compute_cnv_neighbors(adata[, run_pca, copy])	Compute the CNV PCA and neighbor graph used for clustering.
export_cell_groups(adata, output_path, group_key)	Export a Xenium Explorer-compatible cell group CSV.
export_mean_cnv_per_gene(adata, output_path)	Write mean_cnv_per_gene output and return the table.
log_normalize_counts(adata[, input_layer, ...])	Normalize and log-transform a layer for infercnvpy input.
mean_cnv_per_gene(adata[, layer, obs_key, ...])	Return mean CNV value per gene for a selected set of cells.
normalize_counts(adata[, input_layer, ...])	Normalize counts and store them in a layer.
prepare_cnv_input(adata[, raw_layer, ...])	Run the standard InSituCNV preprocessing chain.
run_infercnv(adata, reference_key[, ...])	Run infercnvpy.tl.infercnv with manuscript-style defaults.