
Package index
Visualisation
Visualise and visually inspect evolutionary transcriptomics patterns as well as summary statistics.
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plot_signature()
- Plot Transcriptomic Signature
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plot_signature_gene_quantiles()
- Plot Signature Across Gene Expression Quantiles
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plot_signature_multiple()
- Plot Multiple Transcriptomic Signatures
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plot_signature_transformed()
- Plot Signature Under Different Transformations
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plot_contribution()
- Plot Phylostratum Contribution to Transcriptomic Index
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plot_cullen_frey()
- Plot Cullen-Frey Diagram for Distribution Assessment
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plot_distribution_expression()
- Comparing expression levels distributions across developmental stages
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plot_distribution_pTAI()
- Partial TAI Distribution Plotting Functions
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plot_distribution_pTAI_qqplot()
- QQ plot comparing partial TAI distributions across developmental stages against a reference stage
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plot_distribution_strata()
- Plot Distribution of Genes Across Phylostrata
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plot_gatai_results()
- Plot Comprehensive GATAI Results
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plot_gene_heatmap()
- Plot Gene Expression Heatmap
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plot_gene_profiles()
- Plot Individual Gene Expression Profiles
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plot_gene_space()
- Plot Gene Space Using PCA
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plot_mean_var()
- Plot Mean-Variance Relationship
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plot_null_txi_sample()
- Plot Null TXI Sample Distribution
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plot_relative_expression_bar()
- Plot Mean Relative Expression Levels as Barplot
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plot_relative_expression_line()
- Plot Relative Expression Profiles (Line Plot)
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plot_sample_space()
- Plot Sample Space Visualization
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plot_strata_expression()
- Plot Expression Levels by Phylostratum
Statistical tests
Functions for statistical testing of evolutionary transcriptomics patterns (with visualisation).
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stat_early_conservation_test()
- Early Conservation Test
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stat_flatline_test()
- Flat Line Test for Conservation Pattern
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stat_generic_conservation_test()
- Generic Conservation Test Framework
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stat_late_conservation_test()
- Late Conservation Test
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stat_pairwise_test()
- Pairwise Conservation Test
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stat_reductive_hourglass_test()
- Reductive Hourglass Test
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stat_reverse_hourglass_test()
- Reverse Hourglass Test
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BulkPhyloExpressionSet()
- Bulk PhyloExpressionSet Class
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ConservationTestResult()
- Conservation Test Result S7 Class
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PhyloExpressionSetBase()
- PhyloExpressionSet Base Class
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ScPhyloExpressionSet()
- Single-Cell PhyloExpressionSet Class
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TestResult()
- Test Result S7 Class
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Distribution()
- Distribution S7 Class
Data structures-related
Functions to convert between dataframe and BulkPhyloExpressionSet
or ScPhyloExpressionSet
.
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as_BulkPhyloExpressionSet()
- Convert Data to BulkPhyloExpressionSet
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as_ScPhyloExpressionSet()
- Convert Seurat Object to Single-Cell PhyloExpressionSet
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as_data_frame()
- Convert BulkPhyloExpressionSet to Data Frame
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check_PhyloExpressionSet()
- Check if object is a PhyloExpressionSet
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check_BulkPhyloExpressionSet()
- Check if object is a BulkPhyloExpressionSet
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check_ScPhyloExpressionSet()
- Check if object is a ScPhyloExpressionSet
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taxid()
- Retrieve taxonomy categories from NCBI Taxonomy
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TAI()
- Calculate Transcriptomic Age Index (TAI)
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TDI()
- Calculate Transcriptomic Divergence Index (TDI)
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TEI()
- Calculate Transcriptomic Evolutionary Index (TEI)
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TPI()
- Calculate Transcriptomic Polymorphism Index (TPI)
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TXI()
- Calculate Transcriptomic Index (TXI)
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sTXI()
- Calculate Stratum-Specific Transcriptomic Index
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pTXI()
- Calculate Phylostratum-Specific Transcriptomic Index
Expression or index data-related
Functions to transform, normalise, and manipulate expression datasets.
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age.apply()
- Age Category Specific apply Function
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collapse()
- Collapse PhyloExpressionSet Replicates
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destroy_pattern()
- Destroy Phylotranscriptomic Pattern Using GATAI
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diagnose_test_robustness()
- Diagnose Test Robustness
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distributions
- Predefined Distribution Objects
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downsample_expression()
- Downsample Expression Matrix
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exp_p()
- Format P-Value for Scientific Notation
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genes_lowly_expressed()
- Select Lowly Expressed Genes
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genes_top_expr()
- Gene Expression Filtering Functions
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genes_top_mean()
- Select Top Mean Expressed Genes
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genes_top_variance()
- Select Top Variable Genes
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load_example_phyex_set_sc()
- Load Example Single-Cell PhyloExpressionSet
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match_map()
- Match Gene Expression Data with Phylostratum Map
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match_map_sc()
- Match Single-Cell Expression Data with Phylostratum Map
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normalise_stage_expression()
- Normalise Stage Expression Data
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omit_matrix()
- Compute TXI Profiles Omitting Each Gene
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quantile_rank()
- Calculate Quantile Ranks
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rel_exp_matrix()
- Compute Relative Expression Matrix for PhyloExpressionSet
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relative_expression()
- Relative Expression Functions
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remove_genes()
- Remove Genes from PhyloExpressionSet
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reorder_identities()
- Set Identity Order for ScPhyloExpressionSet
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select_genes()
- Select Genes from PhyloExpressionSet
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set_expression()
- Gene Expression Transformation Functions
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set_identities()
- Set Identities for ScPhyloExpressionSet
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strata_enrichment()
- Calculate Phylostratum Enrichment
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transform_counts()
- Transform Expression Counts in PhyloExpressionSet
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tf()
- Short Alias for Transform Counts
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tf_PS()
- Transform Phylostratum Values
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tf_stability()
- Perform Permutation Tests Under Different Transformations
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available_identities()
- Get available identities
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COUNT_TRANSFORMS
- Count Transformation Functions
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PS_colours()
- Generate Phylostratum Colors
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save_gatai_results_pdf()
- Save GATAI Analysis Results to PDF
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print.TestResult
- Print Method for TestResult
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rename_phyex_set()
- Rename a PhyloExpressionSet
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TI_map
- Transcriptomic Index Name Mapping
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TXI_conf_int()
- Confidence Intervals for Transcriptomic Index (TXI)
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TXI_std_dev()
- Standard Deviation for TXI
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example_phyex_set
- Example phyex set
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example_phyex_set_old
- Example phyex set old