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glyread

ANALYTICS
Velocity0.0

Read and process glycomics and glycoproteomics data

github.com/glycoverse/glyread ↗

glyread now hands every importer's output straight to Bioconductor.

glycomicsdata importbioconductorbreaking changesfile formats
◆Current state
glyread is the import layer, converting output from pGlyco3, Byonic, GlycanFinder, GlyHunter, and pGlycoQuant into glycoverse objects. Version 0.12.0 changed what those objects are: every read_*() function now returns GlycomicSE or GlycoproteomicSE, and 0.12.1 raised the glyexp floor to 0.16.0 to match. Earlier releases in the window went to format handling, particularly multi-glycosite glycopeptides and linkage-specific derivatization presets.
◆Where it's heading
As the stack's entry point, glyread absorbs container decisions first and hardest: because it constructs the objects everything downstream consumes, it had no compatibility path and simply switched return types. The other visible thread is coverage of upstream software, adding importers and presets as new search engines and protocols appear. Those two threads rarely interact.
◆Prediction
Expect the next releases to return to importer coverage, adding formats or presets, now that the container question is settled at the source.

◆Recent moves

  1. 1mo ago

    Minimum glyexp version raised to 0.16.0

    A dependency floor bump matching the container migration that landed in 0.12.0. Bookkeeping that prevents a mismatched install rather than a change in behavior.

    View source ↗
  2. 1mo ago

    All read_*() functions return SummarizedExperiment objects

    Every importer now returns GlycomicSE or GlycoproteomicSE instead of the legacy experiment(). Because glyread constructs the objects the rest of the stack consumes, this is where the migration becomes unavoidable for users: code reading legacy fields must move to assays, rowData, colData, and metadata.

    View source ↗
  3. 3mo ago

    Multi-glycosite glycopeptides get an expand-or-drop option

    The two Byonic importers gain a multisite parameter controlling whether glycopeptides carrying several glycosites are expanded into one row per site or dropped, alongside a fix for handling them at all. A real analytical choice rather than a parsing detail, since the two options give different denominators downstream.

    View source ↗
  4. 3mo ago

    read_glyhunter() gains a derivatization preset

    A preset parameter adds support for glycomics data using sialic acid linkage-specific methylamidation, extending the importer to a protocol it previously could not read correctly, plus a fix for an unused name converter.

    View source ↗
  5. 4mo ago

    glyread 0.9.2

    A release entry with no changelog content beyond the version bump itself. Nothing user-visible is recorded for 0.9.2.

    View source ↗
  6. 6mo ago

    Dependency strategy update

    A packaging-only change to how dependencies are resolved, shipped across the glycoverse packages the same week. No effect on import behavior.

    View source ↗