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Preparing data

aggregate_counts()
Utility function to make reference gene expression profiles

CNV detection

get_bulk()
Aggregate single-cell data into combined bulk expression and allele profile
analyze_bulk()
Call CNVs in a pseudobulk profile using the Numbat joint HMM
detect_clonal_loh()
Call clonal LOH using SNP density. Rcommended for cell lines or tumor samples with no normal cells.

Single-cell clonal decomposition

run_numbat()
Run workflow to decompose tumor subclones

Visualizing results

Numbat
Numbat R6 class
plot_bulks()
Plot a group of pseudobulk HMM profiles
plot_consensus()
Plot consensus CNVs
plot_exp_roll()
Plot single-cell smoothed expression magnitude heatmap
plot_mut_history()
Plot mutational history
plot_phylo_heatmap()
Plot single-cell CNV calls along with the clonal phylogeny
plot_psbulk()
Plot a pseudobulk HMM profile
plot_sc_tree()
Plot single-cell smoothed expression magnitude heatmap