acen_hg19	acen_hg19
acen_hg38	acen_hg38
aggregate_counts	aggregate_counts
analyze_bulk	analyze_bulk
annotate_genes	annotate_genes
annot_consensus	annot_consensus
annot_haplo_segs	annot_haplo_segs
annot_ref	annot_ref
annot_segs	annot_segs
annot_theta_mle	annot_theta_mle
annot_theta_roll	annot_theta_roll
approx_phi_post	approx_phi_post
approx_theta_post	approx_theta_post
binary_entropy	binary_entropy
bulk_example	bulk_example
calc_allele_lik	calc_allele_lik
calc_allele_LLR	calc_allele_LLR
calc_cluster_dist	calc_cluster_dist
calc_exp_LLR	calc_exp_LLR
calc_phi_mle_lnpois	calc_phi_mle_lnpois
check_allele_df	check_allele_df
check_contam	check_contam
check_exp_noise	check_exp_noise
check_exp_ref	check_exp_ref
check_gtf_input	check_gtf_input
check_matrix	check_matrix
check_segs_fix	check_segs_fix
check_segs_loh	check_segs_loh
choose_ref_cor	choose_ref_cor
chrom_sizes_hg19	chrom_sizes_hg19
chrom_sizes_hg38	chrom_sizes_hg38
classify_alleles	classify_alleles
cnv_heatmap	cnv_heatmap
combine_bulk	combine_bulk
compute_posterior	compute_posterior
contract_nodes	contract_nodes
count_mat_example	count_mat_example
count_mat_ref	count_mat_ref
detect_clonal_loh	detect_clonal_loh
df_allele_example	df_allele_example
expand_states	expand_states
exp_hclust	exp_hclust
fill_neu_segs	fill_neu_segs
filter_genes	filter_genes
find_common_diploid	find_common_diploid
fit_bbinom	fit_bbinom
fit_gamma	fit_gamma
fit_lnpois	fit_lnpois
fit_ref_sse	fit_ref_sse
fit_snp_rate	fit_snp_rate
gaps_hg19	gaps_hg19
gaps_hg38	gaps_hg38
generate_postfix	generate_postfix
genotype	genotype
get_allele_bulk	get_allele_bulk
get_allele_hmm	get_allele_hmm
get_allele_post	get_allele_post
get_bulk	get_bulk
get_clone_post	get_clone_post
get_exp_bulk	get_exp_bulk
get_exp_likelihoods	get_exp_likelihoods
get_exp_post	get_exp_post
get_exp_sc	get_exp_sc
get_gtree	get_gtree
get_haplotype_post	get_haplotype_post
get_internal_nodes	get_internal_nodes
get_inter_cm	get_inter_cm
get_joint_post	get_joint_post
get_lambdas_bar	get_lambdas_bar
get_move_cost	get_move_cost
get_move_opt	get_move_opt
get_nodes_celltree	get_nodes_celltree
get_ordered_tips	get_ordered_tips
get_segs_consensus	get_segs_consensus
get_segs_neu	get_segs_neu
get_snps	get_snps
get_tree_post	get_tree_post
gexp_roll_example	gexp_roll_example
gtf_hg19	gtf_hg19
gtf_hg38	gtf_hg38
gtf_mm10	gtf_mm10
hc_example	hc_example
joint_post_example	joint_post_example
label_edges	label_edges
label_genotype	label_genotype
log_mem	log_mem
log_message	log_message
make_group_bulks	make_group_bulks
mark_tumor_lineage	mark_tumor_lineage
Modes	Modes
mut_graph_example	mut_graph_example
Numbat	Numbat
phi_hat_roll	phi_hat_roll
phi_hat_seg	phi_hat_seg
phylogeny_example	phylogeny_example
plot_bulks	plot_bulks
plot_consensus	plot_consensus
plot_exp_roll	plot_exp_roll
plot_mut_history	plot_mut_history
plot_phylo_heatmap	plot_phylo_heatmap
plot_psbulk	plot_psbulk
plot_sc_tree	plot_sc_tree
pnorm.range.log	pnorm.range.log
preprocess_allele	preprocess_allele
pre_likelihood_hmm	pre_likelihood_hmm
ref_hca	ref_hca
ref_hca_counts	ref_hca_counts
relevel_chrom	relevel_chrom
resolve_cnvs	resolve_cnvs
retest_bulks	retest_bulks
retest_cnv	retest_cnv
return_missing_columns	return_missing_columns
run_group_hmms	run_group_hmms
run_numbat	run_numbat
segs_example	segs_example
simes_p	simes_p
simplify_history	simplify_history
smooth_expression	smooth_expression
smooth_segs	smooth_segs
switch_prob_cm	switch_prob_cm
test_multi_allelic	test_multi_allelic
theta_hat_roll	theta_hat_roll
theta_hat_seg	theta_hat_seg
transfer_links	transfer_links
t_test_pval	t_test_pval
upgma	upgma
vcf_meta	vcf_meta
viterbi_loh	viterbi_loh
