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 |
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 |