glyexp 0.16.0

Breaking changes

• toy_experiment has been removed.
• real_experiment and real_experiment2 now use GlycoproteomicSE and GlycomicSE containers, respectively. (#28)

New features

• Tidy manipulation verbs (filter_*(), mutate_*(), select_*(), arrange_*(), rename_*(), slice_*(), and *_join_*()) now accept SummarizedExperiment objects, exposing dimension identifiers as virtual .sample and .variable columns while retaining existing experiment() behavior. (#25)

Minor improvements and bug fixes

• Dplyr-style manipulation helpers now use _col() and _row() suffixes; the former _obs() and _var() names remain available with a soft-deprecation warning. (#29)
• The legacy experiment() container constructor, conversion helpers, accessors, metadata helpers, dimension helpers, and S3 methods are now deprecated. Use GlycomicSE() or GlycoproteomicSE() as the default data container. The dplyr-style manipulation functions remain available. (#26)
• filter_col() and filter_row() now preserve unused factor levels by default; set .drop_levels = TRUE to drop them. (#30)
• standardize_variable() now supports GlycomicSE and GlycoproteomicSE inputs. (#24)