BulkPhyloExpressionSet
                        Bulk PhyloExpressionSet Class
BulkPhyloExpressionSet_from_df
                        Convert Data to BulkPhyloExpressionSet
COUNT_TRANSFORMS        Count Transformation Functions
ConservationTestResult
                        Conservation Test Result S7 Class
Distribution            Distribution S7 Class
PS_colours              Generate Phylostratum Colors
PhyloExpressionSetBase
                        PhyloExpressionSet Base Class
ScPhyloExpressionSet    Single-Cell PhyloExpressionSet Class
ScPhyloExpressionSet_from_matrix
                        Create Single-Cell PhyloExpressionSet from
                        Expression Matrix
ScPhyloExpressionSet_from_seurat
                        Convert Seurat Object to Single-Cell
                        PhyloExpressionSet
TAI                     Calculate Transcriptomic Age Index (TAI)
TDI                     Calculate Transcriptomic Divergence Index (TDI)
TEI                     Calculate Transcriptomic Evolutionary Index
                        (TEI)
TI_map                  Transcriptomic Index Name Mapping
TPI                     Calculate Transcriptomic Polymorphism Index
                        (TPI)
TXI                     Calculate Transcriptomic Index (TXI)
TXI_conf_int            Confidence Intervals for Transcriptomic Index
                        (TXI)
TXI_std_dev             Standard Deviation for TXI
TestResult              Test Result S7 Class
age.apply               Age Category Specific apply Function
as_BulkPhyloExpressionSet
                        as_BulkPhyloExpressionSet
as_data_frame           Convert BulkPhyloExpressionSet to Data Frame
check_BulkPhyloExpressionSet
                        Check if object is a BulkPhyloExpressionSet
check_PhyloExpressionSet
                        Check if object is a PhyloExpressionSet
check_ScPhyloExpressionSet
                        Check if object is a ScPhyloExpressionSet
collapse                Collapse PhyloExpressionSet Replicates
destroy_pattern         Destroy Phylotranscriptomic Pattern Using GATAI
diagnose_test_robustness
                        Diagnose Test Robustness
distributions           Predefined Distribution Objects
downsample              Downsample ScPhyloExpressionSet
downsample_expression   Downsample Expression Matrix by Groups
example_phyex_set       Example phyex set
example_phyex_set_old   Example phyex set old
example_phyex_set_sc    Load Example Single-Cell PhyloExpressionSet
exp_p                   Format P-Value for Scientific Notation
gatai_animate_destruction
                        Animate GATAI Destruction Process
genes_lowly_expressed   Select Lowly Expressed Genes
genes_top_expr          Gene Expression Filtering Functions
genes_top_mean          Select Top Mean Expressed Genes
genes_top_variance      Select Top Variable Genes
get_phylomap            Extract Phylomap from PhyloExpressionSet
get_strata_legend       Get Strata Legend from PhyloExpressionSet
match_map               Match Gene Expression Data with Phylostratum
                        Map
match_map_sc_matrix     Match Expression Matrix with Phylostratum Map
match_map_sc_seurat     Match Single-Cell Expression Data with
                        Phylostratum Map (Seurat)
normalise_stage_expression
                        Normalise Stage Expression Data
omit_matrix             Compute TXI Profiles Omitting Each Gene
pTXI                    Calculate Phylostratum-Specific Transcriptomic
                        Index
permute_PS              Permute Strata in PhyloExpressionSet
plot_contribution       Plot Phylostratum Contribution to
                        Transcriptomic Index
plot_cullen_frey        Plot Cullen-Frey Diagram for Distribution
                        Assessment
plot_distribution_expression
                        Comparing expression levels distributions
                        across developmental stages
plot_distribution_pTAI
                        Partial TAI Distribution Plotting Functions
plot_distribution_pTAI_qqplot
                        QQ plot comparing partial TAI distributions
                        across developmental stages against a reference
                        stage
plot_distribution_strata
                        Plot Distribution of Genes Across Phylostrata
plot_gatai_results      Plot Comprehensive GATAI Results
plot_gene_heatmap       Plot Gene Expression Heatmap
plot_gene_profiles      Plot Individual Gene Expression Profiles
plot_gene_space         Plot Gene Space Using PCA
plot_mean_var           Plot Mean-Variance Relationship
plot_null_txi_sample    Plot Null TXI Sample Distribution
plot_relative_expression_bar
                        Plot Mean Relative Expression Levels as Barplot
plot_relative_expression_line
                        Plot Relative Expression Profiles (Line Plot)
plot_sample_space       Plot Sample Space Visualization
plot_signature          Plot Transcriptomic Signature
plot_signature_gene_quantiles
                        Plot Signature Across Gene Expression Quantiles
plot_signature_multiple
                        Plot Multiple Transcriptomic Signatures
plot_signature_transformed
                        Plot Signature Under Different Transformations
plot_strata_expression
                        Plot Expression Levels by Phylostratum
quantile_rank           Calculate Quantile Ranks
rel_exp_matrix          Compute Relative Expression Matrix for
                        PhyloExpressionSet
relative_expression     Relative Expression Functions
remove_genes            Remove Genes from PhyloExpressionSet
rename_phyex_set        Rename a PhyloExpressionSet
sTXI                    Calculate Stratum-Specific Transcriptomic Index
save_gatai_results_pdf
                        Save GATAI Analysis Results to PDF
select_genes            Select Genes from PhyloExpressionSet
set_expression          Gene Expression Transformation Functions
stat_early_conservation_test
                        Early Conservation Test
stat_flatline_test      Flat Line Test for Conservation Pattern
stat_generic_conservation_test
                        Generic Conservation Test Framework
stat_late_conservation_test
                        Late Conservation Test
stat_pairwise_test      Pairwise Conservation Test
stat_reductive_hourglass_test
                        Reductive Hourglass Test
stat_reverse_hourglass_test
                        Reverse Hourglass Test
strata_enrichment       Calculate Phylostratum Enrichment
taxid                   Retrieve taxonomy categories from NCBI Taxonomy
tf                      Short Alias for Transform Counts
tf_PS                   Transform Phylostratum Values
tf_stability            Perform Permutation Tests Under Different
                        Transformations
transform_counts        Transform Expression Counts in
                        PhyloExpressionSet
