Package: glyfun
Title: Glycan-Centric Functional Enrichment Analysis
Version: 0.1.3
Authors@R: 
    person("Bin", "Fu", , "23110220018@m.fudan.edu.cn", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-8567-2997"))
Description: Provides functional enrichment analysis for
        glycoproteomics data, including both protein-centric and
        glycan-centric approaches. The 'enrich_xxx()' functions answer
        "Which functions are enriched for proteins with dysregulated
        glycosylation?" (traditional protein-level enrichment), while
        'enrich_gc_xxx()' functions answer "Which functions are
        enriched for dysregulated glycan traits?" (glycan-centric,
        linking glycan traits like core-fucosylation with functional
        annotations). Supports both Over Representation Analysis (ORA)
        and Gene Set Enrichment Analysis (GSEA) with common databases
        including GO, KEGG, Reactome, WikiPathways, DO (Disease
        Ontology), and NCG (Network of Cancer Genes). Integrates
        seamlessly with 'glydet' (for site-specific derived traits) and
        'glystats' (for differential expression analysis).
License: MIT + file LICENSE
Suggests: org.Hs.eg.db, ReactomePA, DOSE, GOSemSim, glyexp (>= 0.16.0),
        glyrepr, glyclean, glydet, testthat (>= 3.0.0), S4Vectors,
        knitr, rmarkdown
Config/testthat/edition: 3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
URL: https://glycoverse.github.io/glyfun/
Imports: checkmate, cli, clusterProfiler, dplyr, glystats (>= 0.8.0),
        purrr, rlang, SummarizedExperiment, tibble, tidyselect
VignetteBuilder: knitr
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://glycoverse.r-universe.dev
Date/Publication: 2026-07-16 10:59:53 UTC
RemoteUrl: https://github.com/glycoverse/glyfun
RemoteRef: v0.1.3
RemoteSha: 8a7e2e7c16624a5113b590c5a1ea09f10b7a5dfa
NeedsCompilation: no
Packaged: 2026-07-16 11:49:29 UTC; root
Author: Bin Fu [aut, cre] (ORCID: <https://orcid.org/0000-0001-8567-2997>)
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Depends: R (>= 4.1.0)