LoginSign Up
← Back to all sparks
G

glyfun

ANALYTICS
Velocity0.0

Glycan-Centric Functional Enrichment Analysis

github.com/glycoverse/glyfun ↗

glyfun is three releases old and has spent all of them chasing glyexp's container change.

glycomicsenrichment analysisbioconductorr packagespackage split
◆Current state
glyfun is the newest glycoverse package, carved out to hold the enrichment analysis functions that glystats deprecated. Its entire visible history is the 0.1.x series, and all three releases are container plumbing: detected_universe() learning to accept GlycoproteomicSE, then the vignette and documentation following. There is no independent feature work in the record yet.
◆Where it's heading
This is a package being born into a migration rather than one navigating it. Because glystats removed its gly_enrich_*() functions outright and glysmith already routes enrichment through glyfun, the functional surface is inherited rather than designed here. The near-term arc is catching up to the rest of the stack; the interesting question is what glyfun adds once it is no longer just the relocation target.
◆Prediction
Expect the first release with genuinely new enrichment capability rather than migration plumbing, most likely broadening the gene-set sources glystats never covered.

◆Recent moves

  1. 1mo ago

    Docs move to GlycoproteomicSE inputs

    Documentation and vignettes switch to GlycoproteomicSE and SummarizedExperiment accessors, closing glyfun's part of the Stage II migration. No code change.

    View source ↗
  2. 1mo ago

    Vignette runs against both container types

    The vignette is made to run under both the legacy experiment() and the current SummarizedExperiment containers. A verification step in the same migration rather than a user-visible change.

    View source ↗
  3. 1mo ago

    detected_universe() accepts GlycoproteomicSE objects

    The package's one functional change in the window: detected_universe(), which defines the background set for enrichment tests, accepts GlycoproteomicSE while keeping experiment() support. It is the minimum needed for glyfun to be usable from a migrated pipeline.

    View source ↗