# Haplotype-Aware CNV Analysis from scRNA-Seq

## Documentation for package ‘numbat’ version 1.3.0

- DESCRIPTION file.

## Help Pages

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
annotate_genes | Annotate genes on allele dataframe
annot_ref | example reference cell annotation
bulk_example | example pseudobulk dataframe
check_segs_loh | Check the format of a given clonal LOH segment 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
Numbat | Numbat R6 class
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