v2.1.0.9000

myTAI 2.1.0.9000

Major Refactoring and New Features

• Single-cell support: New ScPhyloExpressionSet S7 class for single-cell data, alongside BulkPhyloExpressionSet for bulk data.
• Property renaming: conditions → identities (and conditions_label → identities_label), counts/counts_collapsed → expression/expression_collapsed.
• All core logic and plotting now robust to both bulk and single-cell objects.

Function Renaming and Prefixes

• Statistical tests: All core test functions now use the stat_ prefix:
  • flatline_test() → stat_flatline_test()
  • early_conservation_test() → stat_early_conservation_test()
  • late_conservation_test() → stat_late_conservation_test()
  • reductive_hourglass_test() → stat_reductive_hourglass_test()
  • reverse_hourglass_test() → stat_reverse_hourglass_test()
  • pairwise_test() → stat_pairwise_test()
  • generic_conservation_test() → stat_generic_conservation_test()
  • generate_conservation_txis() → stat_generate_conservation_txis()
• Gene selection/filtering: All gene selection/filtering functions now use the genes_ prefix:
  • top_expression_genes() → genes_top_mean()
  • top_variance_genes() → genes_top_variance()
  • lowly_expressed_genes() → genes_lowly_expressed()
  • filter_dyn_expr() → genes_filter_dynamic()

Other Changes

• Many internal and Rd files renamed for consistency (e.g., gene_patterns.R → genes_patterns.R, S7_utils.R → utils_S7.R).
• Deprecated/legacy files removed: expression_utils.R, single_cell.R.
• All documentation and examples updated to use new function/property names.