Package: myTAI
Type: Package
Title: Evolutionary Transcriptomics
Version: 2.3.4
Date: 2025-11-10
Maintainer: Hajk-Georg Drost <hajk-georg.drost@tuebingen.mpg.de>
Authors@R: c(person("Hajk-Georg", "Drost",
                role = c("aut", "cre"),
                email = "hajk-georg.drost@tuebingen.mpg.de",
                comment = c(ORCID = "0000-0002-1567-306X")),
              person(given = "Stefan",
                family = "Manolache",
                role = c("aut", "ctb"),
                email = "2648894@dundee.ac.uk",
                comment = c(ORCID = "0009-0006-3326-985X")),
              person(given = "Jaruwatana Sodai", 
                family = "Lotharukpong", 
                role = c("aut", "ctb"), 
                email = "jaruwatana.lotharukpong@tuebingen.mpg.de", 
                comment = c(ORCID = "0000-0002-3475-0980")),
              person(given = "Nikola", 
                family = "Kalábová",
                role = c("aut", "ctb"), 
                email = "nikola@kalabova.eu", 
                comment = c(ORCID = "0009-0007-6384-8809")),
                person(given = "Filipa", 
                family = "Martins Costa",
                role = c("aut", "ctb"), 
                email = "up202301003@edu.fc.up.pt"),
              person(given = "Kristian K",
                family = "Ullrich",
                role = c("aut", "ctb"),
                email = "ullrich@evolbio.mpg.de",
                comment = c(ORCID = "0000-0003-4308-9626")))
Description: 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. 
NeedsCompilation: yes
License: GPL-2
Depends: R (>= 4.1)
Imports: S7, patchwork, purrr, tidyr, Rcpp, memoise, fitdistrplus (>=
        1.1-5), dplyr (>= 0.3.0), RColorBrewer (>= 1.1-2), ggplot2 (>=
        1.0.1), ggforce, ggridges, ggtext, readr (>= 0.2.2), tibble,
        ggplotify, ggrepel, Matrix, pheatmap
Suggests: knitr (>= 1.6), rmarkdown (>= 0.3.3), testthat (>= 0.9.1),
        mgcv, Seurat, SeuratObject, uwot, decor, DESeq2, gganimate,
        taxize
LinkingTo: RcppArmadillo, RcppThread, Rcpp
URL: https://drostlab.github.io/myTAI/
BugReports: https://github.com/drostlab/myTAI/issues
RoxygenNote: 7.3.3
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
VignetteBuilder: knitr
Collate: 'globals.R' 'utils_S7.R' 'utils_math.R' 'phyloset_base.R'
        'phyloset_bulk.R' 'phyloset_sc.R' 'stat_distributions.R'
        'stat_test_result.R' 'RcppExports.R' 'age.apply.R' 'datasets.R'
        'destroy_pattern.R' 'gatai_convergence_plots.R'
        'genes_filter.R' 'genes_patterns.R' 'genes_transforms.R'
        'myTAI-package.R' 'omit_matrix.R' 'plot_contribution.R'
        'plot_distribution_expression.R' 'plot_distribution_pTAI.R'
        'plot_distribution_strata.R' 'plot_gene_heatmap.R'
        'plot_gene_profiles.R' 'plot_gene_space.R' 'plot_mean_var.R'
        'plot_relative_expression.R' 'plot_sample_space.R'
        'plot_signature.R' 'plot_signature_gene_quantiles.R'
        'plot_signature_multiple.R' 'plot_signature_transformed.R'
        'plot_strata_expression.R' 'plot_utils.R'
        'stat_ci_estimation.R' 'stat_early_conservation_test.R'
        'stat_flatline_test.R' 'stat_generic_conservation_test.R'
        'stat_late_conservation_test.R' 'stat_null_conservation_txis.R'
        'stat_pairwise_test.R' 'stat_reductive_hourglass_test.R'
        'stat_reverse_hourglass_test.R' 'taxid.R' 'tf_PS.R'
        'tf_stability.R' 'zzz.R'
Packaged: 2025-11-11 09:54:33 UTC; hdrost001
Author: Hajk-Georg Drost [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1567-306X>),
  Stefan Manolache [aut, ctb] (ORCID:
    <https://orcid.org/0009-0006-3326-985X>),
  Jaruwatana Sodai Lotharukpong [aut, ctb] (ORCID:
    <https://orcid.org/0000-0002-3475-0980>),
  Nikola Kalábová [aut, ctb] (ORCID:
    <https://orcid.org/0009-0007-6384-8809>),
  Filipa Martins Costa [aut, ctb],
  Kristian K Ullrich [aut, ctb] (ORCID:
    <https://orcid.org/0000-0003-4308-9626>)
Repository: CRAN
Date/Publication: 2025-11-11 11:10:02 UTC
Built: R 4.6.0; x86_64-w64-mingw32; 2026-01-05 19:24:00 UTC; windows
Archs: x64
