Haplotype-Aware CNV Analysis from scRNA-Seq

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Documentation for package ‘numbat’ version 1.3.0

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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