age.apply               Age Category Specific apply Function
as_BulkPhyloExpressionSet
                        as_BulkPhyloExpressionSet
as_data_frame           Convert BulkPhyloExpressionSet to Data Frame
BulkPhyloExpressionSet
                        Bulk PhyloExpressionSet Class
BulkPhyloExpressionSet_from_df
                        Convert Data to BulkPhyloExpressionSet
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
ConservationTestResult
                        Conservation Test Result S7 Class
COUNT_TRANSFORMS        Count Transformation Functions
destroy_pattern         Destroy Phylotranscriptomic Pattern Using GATAI
diagnose_test_robustness
                        Diagnose Test Robustness
Distribution            Distribution S7 Class
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
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
permute_PS              Permute Strata in PhyloExpressionSet
PhyloExpressionSetBase
                        PhyloExpressionSet Base Class
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
PS_colours              Generate Phylostratum Colors
pTXI                    Calculate Phylostratum-Specific Transcriptomic
                        Index
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
save_gatai_results_pdf
                        Save GATAI Analysis Results to PDF
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
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
sTXI                    Calculate Stratum-Specific Transcriptomic Index
TAI                     Calculate Transcriptomic Age Index (TAI)
taxid                   Retrieve taxonomy categories from NCBI Taxonomy
TDI                     Calculate Transcriptomic Divergence Index (TDI)
TEI                     Calculate Transcriptomic Evolutionary Index
                        (TEI)
TestResult              Test Result S7 Class
tf                      Short Alias for Transform Counts
tf_PS                   Transform Phylostratum Values
tf_stability            Perform Permutation Tests Under Different
                        Transformations
TI_map                  Transcriptomic Index Name Mapping
TPI                     Calculate Transcriptomic Polymorphism Index
                        (TPI)
transform_counts        Transform Expression Counts in
                        PhyloExpressionSet
TXI                     Calculate Transcriptomic Index (TXI)
TXI_conf_int            Confidence Intervals for Transcriptomic Index
                        (TXI)
TXI_std_dev             Standard Deviation for TXI
