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glyfun

glyfun provides functional enrichment analysis for glycoproteomics data. It provides two sets of functions, answering different questions:

  • enrich_xxx(): “Which functions are enriched for proteins with dysregulated glycosylation?”
  • enrich_gc_xxx(): “Which functions are enriched for dyregulated glycan traits?”

gc is for “glycan-centric”, which means connecting glycan traits (e.g. core-fucosylation) with functional annotations.

Both Over Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA) are supported, with common databases including GO, KEGG, Reactome, WikiPathways, DO (Disease Ontology), and NCG (Network of Cancer Genes).

Installation

The glyfun package is not a core glycoverse package. You need to install it individually even if you have installed the meta-package glycoverse.

Note: This package is still in development and not for productive use.

Install the development version (NOT recommended):

pak::pkg_install("glycoverse/glyfun")

Documentation

  • 🚀 Get started: Here
  • 📚 Reference: Here

Role in glycoverse

glyfun integrates seamlessly with glydet (for calculating site-specific derived traits and motif quantification) and glystats (for differential expression analysis). As the final piece of the glycoproteomics analytical puzzle, glyfun bridges the gap between raw glycan quantification and biological insight, enabling researchers to move beyond data processing to functional glycomining.

Example

Comming soon.