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glydet

ANALYTICS
Velocity0.0

Describe Glycosylation Structural Properties in a Site Specific Manner

github.com/glycoverse/glydet ↗

glydet is rebuilding its glycan trait vocabulary on top of someone else's container.

glycomicstrait derivationbioconductorbreaking changesr packages
◆Current state
glydet derives glycan-derived traits from glycomics and glycoproteomics data. The 0.12.x line spent its releases absorbing glyexp's container migration: derive_traits(), quantify_motifs(), and add_meta_properties() now accept GlycomicSE and GlycoproteomicSE natively, with the legacy experiment() path kept only for backward-compatible return types. The substantive feature work sits one release back in 0.11.0, which added sialic acid linkage traits and three published trait sets.
◆Where it's heading
Two threads run in parallel here. One is infrastructure: track glyexp's Stage II migration, drop the underscore matrix interfaces, and converge on a single trait column in var_info. The other is content: keep adding named trait sets from the literature (Clerc 2018, Li 2025, Fu 2026) so users cite a set rather than hand-roll definitions. The LLM-backed explain_trait() and make_trait() helpers are becoming provider-agnostic rather than deeper.
◆Prediction
The trait catalogue is the growth area, so expect more published trait sets added as named functions, and the deprecated basic_traits() and all_traits() aliases to be removed once the container migration settles.

◆Recent moves

  1. 1mo ago

    Docs and vignettes move to SummarizedExperiment inputs

    Documentation-only cleanup closing out Stage II of the glyexp container migration. The examples now show GlycomicSE and GlycoproteomicSE with SummarizedExperiment accessors, matching the code changes that landed in 0.12.0 and 0.12.1.

    View source ↗
  2. 1mo ago

    Trait functions behave consistently across both containers

    add_meta_properties(), derive_traits(), and quantify_motifs() now behave the same whether they are handed a legacy experiment() or a SummarizedExperiment. This is the compatibility layer that lets users upgrade glyexp without their trait pipelines diverging.

    View source ↗
  3. 1mo ago

    Container migration lands alongside batch trait creation

    The migration release: derive_traits_() is removed in favor of container-based calls, quantify_motifs() returns a trait column matching derive_traits(), and the three main entry points accept GlycomicSE and GlycoproteomicSE. make_traits() and explain_traits() add batch creation that marks unrecognized entries NA rather than failing the whole call.

    View source ↗
  4. 1mo ago

    glymotif 0.17 compatibility and clearer trait wording

    A compatibility bump for glymotif 0.17.0 plus plainer wording in explain_trait() for antenna and monosaccharide count predicates. No behavior change for existing pipelines.

    View source ↗
  5. 3mo ago

    Sialic acid linkage traits and three published trait sets

    The most substantive feature release in the window: optional sia_link traits extend traits_basic() and traits_detailed() with linkage-resolved variants, and traits_clerc_2018(), traits_li_2025(), and traits_fu_2026() ship as named literature-derived sets. The AI helpers also become provider-agnostic through ellmer rather than being tied to one vendor.

    View source ↗
  6. 4mo ago

    Variable name standardization and vignette fixes

    derive_traits() standardizes output variable names and two vignette examples are corrected. Housekeeping that predates the container work.

    View source ↗