Numbat                  Numbat R6 class
acen_hg19               centromere regions (hg19)
acen_hg38               centromere regions (hg38)
aggregate_counts        Utility function to make reference gene
                        expression profiles
analyze_bulk            Call CNVs in a pseudobulk profile using the
                        Numbat joint HMM
annot_ref               example reference cell annotation
annotate_genes          Annotate genes on allele dataframe
bulk_example            example pseudobulk dataframe
chrom_sizes_hg19        chromosome sizes (hg19)
chrom_sizes_hg38        chromosome sizes (hg38)
cnv_heatmap             Plot CNV heatmap
count_mat_example       example gene expression count matrix
count_mat_ref           example reference count matrix
detect_clonal_loh       Call clonal LOH using SNP density.  Rcommended
                        for cell lines or tumor samples with no normal
                        cells.
df_allele_example       example allele count dataframe
gaps_hg19               genome gap regions (hg19)
gaps_hg38               genome gap regions (hg38)
get_bulk                Aggregate single-cell data into combined bulk
                        expression and allele profile
get_gtree               Get a tidygraph tree with simplified mutational
                        history.
gexp_roll_example       example smoothed gene expression dataframe
gtf_hg19                gene model (hg19)
gtf_hg38                gene model (hg38)
gtf_mm10                gene model (mm10)
hc_example              example hclust tree
joint_post_example      example joint single-cell cnv posterior
                        dataframe
mut_graph_example       example mutation graph
phylogeny_example       example single-cell phylogeny
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
pre_likelihood_hmm      HMM object for unit tests
ref_hca                 reference expression magnitudes from HCA
ref_hca_counts          reference expression counts from HCA
run_numbat              Run workflow to decompose tumor subclones
segs_example            example CNV segments dataframe
upgma                   UPGMA and WPGMA clustering
vcf_meta                example VCF header
