.collapse_replicates	dot-collapse_replicates
.compute_reduction	dot-compute_reduction
.fit_gamma	dot-fit_gamma
.fit_normal	dot-fit_normal
.get_expression_from_seurat	dot-get_expression_from_seurat
.get_p_value	dot-get_p_value
.memo_generate_conservation_txis	dot-memo_generate_conservation_txis
.plot_gene_heatmap_impl	dot-plot_gene_heatmap_impl
.prepare_sc_plot_data	dot-prepare_sc_plot_data
.pseudobulk_expression	dot-pseudobulk_expression
.pTXI	dot-pTXI
.to_std_expr	dot-to_std_expr
.TXI	dot-TXI
.TXI_sc	dot-TXI_sc
.TXI_sc_adaptive	dot-TXI_sc_adaptive
age.apply	age.apply
as_BulkPhyloExpressionSet	as_BulkPhyloExpressionSet
as_data_frame	as_data_frame
BulkPhyloExpressionSet	BulkPhyloExpressionSet
BulkPhyloExpressionSet_from_df	BulkPhyloExpressionSet_from_df
check_BulkPhyloExpressionSet	check_BulkPhyloExpressionSet
check_PhyloExpressionSet	check_PhyloExpressionSet
check_ScPhyloExpressionSet	check_ScPhyloExpressionSet
collapse	collapse
conf_int	conf_int
consensus	consensus
ConservationTestResult	ConservationTestResult
convergence_plots	convergence_plots
COUNT_TRANSFORMS	COUNT_TRANSFORMS
cpp_txi_sc	cpp_txi_sc
destroy_pattern	destroy_pattern
diagnose_test_robustness	diagnose_test_robustness
Distribution	Distribution
distributions	distributions
downsample	downsample
downsample_expression	downsample_expression
early_gene	early_gene
ec_score	ec_score
example_phyex_set	example_phyex_set
example_phyex_set_old	example_phyex_set_old
example_phyex_set_sc	example_phyex_set_sc
exp_p	exp_p
full_gatai_convergence_plot	full_gatai_convergence_plot
gatai_animate_destruction	gatai_animate_destruction
genes_filter_dynamic	genes_filter_dynamic
genes_lowly_expressed	genes_lowly_expressed
genes_top_expr	genes_top_expr
genes_top_mean	genes_top_mean
genes_top_variance	genes_top_variance
geom_mean	geom_mean
get_angles	get_angles
get_phylomap	get_phylomap
get_strata_legend	get_strata_legend
goodness_of_fit	goodness_of_fit
late_gene	late_gene
lc_score	lc_score
match_map	match_map
match_map_sc_matrix	match_map_sc_matrix
match_map_sc_seurat	match_map_sc_seurat
mid_gene	mid_gene
mod_pi	mod_pi
new_options_property	new_options_property
new_required_property	new_required_property
normalise_stage_expression	normalise_stage_expression
omit_matrix	omit_matrix
pair_score	pair_score
permute_PS	permute_PS
petal_plot	petal_plot
PhyloExpressionSetBase	PhyloExpressionSetBase
plot_contribution	plot_contribution
plot_cullen_frey	plot_cullen_frey
plot_distribution_expression	plot_distribution_expression
plot_distribution_pTAI	plot_distribution_pTAI
plot_distribution_pTAI_qqplot	plot_distribution_pTAI_qqplot
plot_distribution_strata	plot_distribution_strata
plot_gatai_results	plot_gatai_results
plot_gene_heatmap	plot_gene_heatmap
plot_gene_profiles	plot_gene_profiles
plot_gene_space	plot_gene_space
plot_mean_var	plot_mean_var
plot_null_txi_sample	plot_null_txi_sample
plot_relative_expression_bar	plot_relative_expression_bar
plot_relative_expression_line	plot_relative_expression_line
plot_sample_space	plot_sample_space
plot_signature	plot_signature
plot_signature_gene_quantiles	plot_signature_gene_quantiles
plot_signature_multiple	plot_signature_multiple
plot_signature_transformed	plot_signature_transformed
plot_strata_expression	plot_strata_expression
print.TestResult	print.TestResult
PS_colours	PS_colours
pTXI	pTXI
quantile_rank	quantile_rank
reductive_hourglass_score	reductive_hourglass_score
relative_expression	relative_expression
rel_exp_matrix	rel_exp_matrix
remove_genes	remove_genes
rename_phyex_set	rename_phyex_set
reverse_hourglass_score	reverse_hourglass_score
rev_mid_gene	rev_mid_gene
rowVars	rowVars
save_gatai_results_pdf	save_gatai_results_pdf
ScPhyloExpressionSet	ScPhyloExpressionSet
ScPhyloExpressionSet_from_matrix	ScPhyloExpressionSet_from_matrix
ScPhyloExpressionSet_from_seurat	ScPhyloExpressionSet_from_seurat
select_genes	select_genes
set_expression	set_expression
stat_early_conservation_test	stat_early_conservation_test
stat_flatline_test	stat_flatline_test
stat_generate_conservation_txis	stat_generate_conservation_txis
stat_generic_conservation_test	stat_generic_conservation_test
stat_late_conservation_test	stat_late_conservation_test
stat_pairwise_test	stat_pairwise_test
stat_reductive_hourglass_test	stat_reductive_hourglass_test
stat_reverse_hourglass_test	stat_reverse_hourglass_test
strata_enrichment	strata_enrichment
sTXI	sTXI
TAI	TAI
taxid	taxid
TDI	TDI
TEI	TEI
TestResult	TestResult
tf	tf
tf_PS	tf_PS
tf_stability	tf_stability
threshold_comparison_plots	threshold_comparison_plots
TI_map	TI_map
TPI	TPI
transform_counts	transform_counts
TXI	TXI
TXI_conf_int	TXI_conf_int
TXI_std_dev	TXI_std_dev
