Package: myTAI 2.3.7

Hajk-Georg Drost

myTAI: Evolutionary Transcriptomics

Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2018) <doi:10.1093/bioinformatics/btx835>). This package aims to provide a transcriptome analysis environment to quantify the average evolutionary age of genes contributing to a transcriptome of interest.

Authors:Hajk-Georg Drost [aut, cre], Stefan Manolache [aut, ctb], Jaruwatana Sodai Lotharukpong [aut, ctb], Nikola Kalábová [aut, ctb], Filipa Martins Costa [aut, ctb], Kristian K Ullrich [aut, ctb]

myTAI_2.3.7.tar.gz
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myTAI_2.3.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
myTAI/json (API)

# Install 'myTAI' in R:
install.packages('myTAI', repos = c('https://drostlab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/drostlab/mytai/issues

Pkgdown/docs site:https://drostlab.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

biological-processesconservationevo-devoevolutionevolutionary-transcriptomicsexpression-profilesgene-expressiongene-setsmytaistudies-transcriptomestranscriptomecpp

9.83 score 47 stars 122 scripts 708 downloads 4 mentions 85 exports 66 dependencies

Last updated from:4933614c72. Checks:13 OK, 2 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK312
linux-devel-x86_64OK280
source / vignettesOK496
linux-release-arm64OK260
linux-release-x86_64OK316
macos-release-arm64OK234
macos-release-x86_64OK322
macos-oldrel-arm64OK183
macos-oldrel-x86_64OK416
windows-devel-arm64FAIL331
windows-devel-x86_64OK275
windows-release-arm64FAIL394
windows-release-x86_64OK274
windows-oldrel-x86_64OK274
wasm-releaseOK223

Exports:age.applyas_BulkPhyloExpressionSetas_data_frameBulkPhyloExpressionSetBulkPhyloExpressionSet_from_dfcheck_BulkPhyloExpressionSetcheck_PhyloExpressionSetcheck_ScPhyloExpressionSetcollapseConservationTestResultCOUNT_TRANSFORMSdestroy_patterndiagnose_test_robustnessdistributionsdownsampledownsample_expressionexp_pgatai_animate_destructiongenes_lowly_expressedgenes_top_exprgenes_top_meangenes_top_varianceget_phylomapget_strata_legendmatch_mapmatch_map_sc_matrixmatch_map_sc_seuratnormalise_stage_expressionomit_matrixpermute_PSPhyloExpressionSetBaseplot_contributionplot_cullen_freyplot_distribution_expressionplot_distribution_pTAIplot_distribution_pTAI_qqplotplot_distribution_strataplot_gatai_resultsplot_gene_heatmapplot_gene_profilesplot_gene_spaceplot_mean_varplot_null_txi_sampleplot_relative_expression_barplot_relative_expression_lineplot_sample_spaceplot_signatureplot_signature_gene_quantilesplot_signature_multipleplot_signature_transformedplot_strata_expressionPS_colourspTXIquantile_rankrel_exp_matrixrelative_expressionremove_genesrename_phyex_setsave_gatai_results_pdfScPhyloExpressionSetScPhyloExpressionSet_from_matrixScPhyloExpressionSet_from_seuratselect_genesset_expressionstat_early_conservation_teststat_flatline_teststat_late_conservation_teststat_pairwise_teststat_reductive_hourglass_teststat_reverse_hourglass_teststrata_enrichmentsTXITAItaxidTDITEITestResulttftf_PStf_stabilityTPItransform_countsTXITXI_conf_intTXI_std_dev

Dependencies:base64encbitbit64cachemclicliprcpp11crayondigestdplyrfarverfastmapfitdistrplusfsgenericsggforceggplot2ggplotifyggrepelggridgesgluegridGraphicsgtablehmsisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmemoisepatchworkpheatmappillarpkgconfigpolyclipprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppThreadreadrrlangS7scalesstringistringrsurvivalsystemfontstibbletidyrtidyselecttweenrtzdbutf8vctrsviridisLitevroomwithryulab.utils

Obtaining taxonomy information
Taxonomic Information Retrieval | Retrieve Children Nodes
Rendered fromtaxonomy.Rmdusingknitr::rmarkdown

Last update: 2026-05-28
Started: 2025-08-16

Gene age inference
What is genomic phylostratigraphy? | Gene age information in TAI | The debate | Homology search bias | Alternatives to BLASTp | Open questions | Summary
Rendered fromphylostratigraphy.Rmdusingknitr::rmarkdown

Last update: 2026-02-04
Started: 2025-08-04

Getting started
Rendered frommyTAI.Rmdusingknitr::rmarkdown

Last update: 2026-02-04
Started: 2025-08-04

Beautiful plots made via myTAI
Gallery of different plots available with myTAI | Bulk RNA-seq data | myTAI plots can be modified as a ggplot2 object. | Transformation and robustness checks | Statistical tests and plotting results | Average gene expression level by phylostratum | Contribution to the overall TAI by phylostratum | Contribution to the overall TAI by partial TAI (pTAI) | Phylostratum distribution | Expression heatmap | Dimension reduction | At the gene level | At the sample level | Inspecting mean-variance relationship | Individual gene expression profiles | Single cell RNA-seq data | Single-cell signature plots | Other single-cell visualizations
Rendered fromtai-gallery.Rmdusingknitr::rmarkdown

Last update: 2026-01-19
Started: 2025-08-04

Transforming dataset for myTAI
The motivation for transformating of RNA-seq data | Transforming RNA-seq data for myTAI | Other robustness checks | Transforming gene age information for myTAI | Conclusion
Rendered fromtai-transform.Rmdusingknitr::rmarkdown

Last update: 2025-11-11
Started: 2025-08-04

Break TAI patterns using gaTAI
Motivation for breaking the hourglass | Break the hourglass using gaTAI
Rendered fromtai-breaker.Rmdusingknitr::rmarkdown

Last update: 2025-11-10
Started: 2025-08-04

Bring your datasets into myTAI
S7 BulkPhyloExpressionSet and ScPhyloExpressionSet objects | Constructing BulkPhyloExpressionSet and ScPhyloExpressionSet | Loading raw data | Mock (bulk) dataset for BulkPhyloExpressionSet | Bulk RNA-seq data without replicates | What if the dataset contains replicates? | Mock single-cell dataset for ScPhyloExpressionSet | Summary
Rendered fromphylo-expression-object.Rmdusingknitr::rmarkdown

Last update: 2025-11-10
Started: 2025-08-04

Other evolutionary and expression indices
Motivation for non-TAI approaches | Transcriptome divergence index (TDI) | Mock bulk RNA-seq dataset for TDI | Transcriptome specificity index (TSI) | Transcriptome {insert your idea} index | Summary
Rendered fromother-strata.Rmdusingknitr::rmarkdown

Last update: 2025-11-10
Started: 2025-08-04

Statistical testing with myTAI
The motivation for statistically-informed analysis of TAI patterns | Statistical analysis of TAI patterns | Flatline test | Cullen and Frey plot | Null distribution visualisation | Reductive hourglass test and other time-course tests | Reductive hourglass test | Reverse hourglass test | Early conservation test | Late conservation test | Pairwise test | Summary
Rendered fromtai-stats.Rmdusingknitr::rmarkdown

Last update: 2025-11-10
Started: 2025-08-04

Readme and manuals

Help Manual

Help pageTopics
Age Category Specific apply Functionage.apply
as_BulkPhyloExpressionSetas_BulkPhyloExpressionSet
Convert BulkPhyloExpressionSet to Data Frameas_data_frame
Bulk PhyloExpressionSet ClassBulkPhyloExpressionSet
Convert Data to BulkPhyloExpressionSetBulkPhyloExpressionSet_from_df
Check if object is a BulkPhyloExpressionSetcheck_BulkPhyloExpressionSet
Check if object is a PhyloExpressionSetcheck_PhyloExpressionSet
Check if object is a ScPhyloExpressionSetcheck_ScPhyloExpressionSet
Collapse PhyloExpressionSet Replicatescollapse
Conservation Test Result S7 ClassConservationTestResult
Count Transformation FunctionsCOUNT_TRANSFORMS
Destroy Phylotranscriptomic Pattern Using GATAIdestroy_pattern
Diagnose Test Robustnessdiagnose_test_robustness
Distribution S7 ClassDistribution
Predefined Distribution Objectsdistributions
Downsample ScPhyloExpressionSetdownsample
Downsample Expression Matrix by Groupsdownsample_expression
Example phyex setexample_phyex_set
Example phyex set oldexample_phyex_set_old
Load Example Single-Cell PhyloExpressionSetexample_phyex_set_sc
Format P-Value for Scientific Notationexp_p
Animate GATAI Destruction Processgatai_animate_destruction
Select Lowly Expressed Genesgenes_lowly_expressed
Gene Expression Filtering Functionsgenes_top_expr
Select Top Mean Expressed Genesgenes_top_mean
Select Top Variable Genesgenes_top_variance
Extract Phylomap from PhyloExpressionSetget_phylomap
Get Strata Legend from PhyloExpressionSetget_strata_legend
Match Gene Expression Data with Phylostratum Mapmatch_map
Match Expression Matrix with Phylostratum Mapmatch_map_sc_matrix
Match Single-Cell Expression Data with Phylostratum Map (Seurat)match_map_sc_seurat
Normalise Stage Expression Datanormalise_stage_expression
Compute TXI Profiles Omitting Each Geneomit_matrix
Permute Strata in PhyloExpressionSetpermute_PS
PhyloExpressionSet Base ClassPhyloExpressionSetBase
Plot Phylostratum Contribution to Transcriptomic Indexplot_contribution
Plot Cullen-Frey Diagram for Distribution Assessmentplot_cullen_frey
Comparing expression levels distributions across developmental stagesplot_distribution_expression
Partial TAI Distribution Plotting Functionsplot_distribution_pTAI
QQ plot comparing partial TAI distributions across developmental stages against a reference stageplot_distribution_pTAI_qqplot
Plot Distribution of Genes Across Phylostrataplot_distribution_strata
Plot Comprehensive GATAI Resultsplot_gatai_results
Plot Gene Expression Heatmapplot_gene_heatmap
Plot Individual Gene Expression Profilesplot_gene_profiles
Plot Gene Space Using PCAplot_gene_space
Plot Mean-Variance Relationshipplot_mean_var
Plot Null TXI Sample Distributionplot_null_txi_sample
Plot Mean Relative Expression Levels as Barplotplot_relative_expression_bar
Plot Relative Expression Profiles (Line Plot)plot_relative_expression_line
Plot Sample Space Visualizationplot_sample_space
Plot Transcriptomic Signatureplot_signature
Plot Signature Across Gene Expression Quantilesplot_signature_gene_quantiles
Plot Multiple Transcriptomic Signaturesplot_signature_multiple
Plot Signature Under Different Transformationsplot_signature_transformed
Plot Expression Levels by Phylostratumplot_strata_expression
Generate Phylostratum ColorsPS_colours
Calculate Phylostratum-Specific Transcriptomic IndexpTXI
Calculate Quantile Ranksquantile_rank
Compute Relative Expression Matrix for PhyloExpressionSetrel_exp_matrix
Relative Expression Functionsrelative_expression
Remove Genes from PhyloExpressionSetremove_genes
Rename a PhyloExpressionSetrename_phyex_set
Save GATAI Analysis Results to PDFsave_gatai_results_pdf
Single-Cell PhyloExpressionSet ClassScPhyloExpressionSet
Create Single-Cell PhyloExpressionSet from Expression MatrixScPhyloExpressionSet_from_matrix
Convert Seurat Object to Single-Cell PhyloExpressionSetScPhyloExpressionSet_from_seurat
Select Genes from PhyloExpressionSetselect_genes
Gene Expression Transformation Functionsset_expression
Early Conservation Teststat_early_conservation_test
Flat Line Test for Conservation Patternstat_flatline_test
Generic Conservation Test Frameworkstat_generic_conservation_test
Late Conservation Teststat_late_conservation_test
Pairwise Conservation Teststat_pairwise_test
Reductive Hourglass Teststat_reductive_hourglass_test
Reverse Hourglass Teststat_reverse_hourglass_test
Calculate Phylostratum Enrichmentstrata_enrichment
Calculate Stratum-Specific Transcriptomic IndexsTXI
Calculate Transcriptomic Age Index (TAI)TAI
Retrieve taxonomy categories from NCBI Taxonomytaxid
Calculate Transcriptomic Divergence Index (TDI)TDI
Calculate Transcriptomic Evolutionary Index (TEI)TEI
Test Result S7 ClassTestResult
Short Alias for Transform Countstf
Transform Phylostratum Valuestf_PS
Perform Permutation Tests Under Different Transformationstf_stability
Transcriptomic Index Name MappingTI_map
Calculate Transcriptomic Polymorphism Index (TPI)TPI
Transform Expression Counts in PhyloExpressionSettransform_counts
Calculate Transcriptomic Index (TXI)TXI
Confidence Intervals for Transcriptomic Index (TXI)TXI_conf_int
Standard Deviation for TXITXI_std_dev