# Evolutionary Transcriptomics

## Documentation for package ‘myTAI’ version 2.3.4

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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
relative_expression | Relative Expression Functions
rel_exp_matrix | Compute Relative Expression Matrix for PhyloExpressionSet
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