Package: glyfun 0.1.3

Bin Fu

glyfun: Glycan-Centric Functional Enrichment Analysis

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).

Authors:Bin Fu [aut, cre]

glyfun_0.1.3.tar.gz
glyfun_0.1.3.zip(r-4.7)glyfun_0.1.3.zip(r-4.6)glyfun_0.1.3.zip(r-4.5)
glyfun_0.1.3.tgz(r-4.6-any)glyfun_0.1.3.tgz(r-4.5-any)
glyfun_0.1.3.tar.gz(r-4.7-any)glyfun_0.1.3.tar.gz(r-4.6-any)
glyfun_0.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
glyfun/json (API)

# Install 'glyfun' in R:

install.packages('glyfun', repos = c('https://glycoverse.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/glycoverse/glyfun/issues

Pkgdown/docs site:https://glycoverse.github.io

On CRAN:

3.48 score 25 exports 142 dependencies

Last updated from:8a7e2e7c16 (on v0.1.3). Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	383
source / vignettes	OK	394
linux-release-x86_64	OK	390
macos-release-arm64	OK	188
macos-oldrel-arm64	OK	192
windows-devel	OK	291
windows-release	OK	280
windows-oldrel	OK	290
wasm-release	OK	267

Exports:detected_universe enrich_gc_gsea_do enrich_gc_gsea_go enrich_gc_gsea_kegg enrich_gc_gsea_ncg enrich_gc_gsea_reactome enrich_gc_gsea_wp enrich_gc_ora_do enrich_gc_ora_go enrich_gc_ora_kegg enrich_gc_ora_ncg enrich_gc_ora_reactome enrich_gc_ora_wp enrich_gsea_do enrich_gsea_go enrich_gsea_kegg enrich_gsea_ncg enrich_gsea_reactome enrich_gsea_wp enrich_ora_do enrich_ora_go enrich_ora_kegg enrich_ora_ncg enrich_ora_reactome enrich_ora_wp

Dependencies:abind aisdk AnnotationDbi ape aplot askpass backports base64enc Biobase BiocGenerics Biostrings bit bit64 blob broom bslib cachem callr checkmate cli cluster clusterProfiler cpp11 crayon curl DBI DelayedArray digest DOSE dplyr enrichit enrichplot evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver fs gdtools generics GenomicRanges ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree glue glyexp glyrepr glystats GO.db GOSemSim gridGraphics gson gtable highr hms htmltools htmlwidgets httr httr2 igraph IRanges isoband janitor jquerylib jsonlite KEGGREST knitr labeling lattice lazyeval lifecycle lubridate magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nlme openssl otel patchwork pillar pkgconfig plyr png polyclip processx ps purrr qvalue R6 rappdirs RColorBrewer Rcpp RcppEigen reshape2 rlang rmarkdown RSQLite rstackdeque S4Arrays S4Vectors S7 sass scales scatterpie Seqinfo snakecase SparseArray stringi stringr SummarizedExperiment survival sys systemfonts tibble tidydr tidyr tidyselect tidytree timechange tinytex treeio tweenr utf8 vctrs viridisLite withr xfun XVector yaml yulab.utils

Get Started with glyfun

Approach 1: Protein-Centric Enrichment Analysis | Over Representation Analysis (ORA) | Gene Set Enrichment Analysis (GSEA) | Approach 2: Glycan-Centric Enrichment Analysis

Rendered fromglyfun.Rmdusingknitr::rmarkdown

Last update: 2026-07-16
Started: 2026-04-25

Help page	Topics
Helper function to prepare the 'universe' parameter	detected_universe
Glycan-Centric Disease Ontology (DO) Gene Set Enrichment Analysis	enrich_gc_gsea_do
Glycan-Centric GO Gene Set Enrichment Analysis	enrich_gc_gsea_go
Glycan-Centric KEGG Gene Set Enrichment Analysis	enrich_gc_gsea_kegg
Glycan-Centric Network of Cancer Genes (NCG) Gene Set Enrichment Analysis	enrich_gc_gsea_ncg
Glycan-Centric Reactome Gene Set Enrichment Analysis	enrich_gc_gsea_reactome
Glycan-Centric WikiPathways Gene Set Enrichment Analysis	enrich_gc_gsea_wp
Glycan-Centric Disease Ontology (DO) Over Representation Analysis	enrich_gc_ora_do
Glycan-Centric GO Over Representation Analysis	enrich_gc_ora_go
Glycan-Centric KEGG Over Representation Analysis	enrich_gc_ora_kegg
Glycan-Centric Network of Cancer Genes (NCG) Over Representation Analysis	enrich_gc_ora_ncg
Glycan-Centric Reactome Pathway Over Representation Analysis	enrich_gc_ora_reactome
Glycan-Centric WikiPathways Over Representation Analysis	enrich_gc_ora_wp
Disease Ontology (DO) Gene Set Enrichment Analysis	enrich_gsea_do
GO Gene Set Enrichment Analysis	enrich_gsea_go
KEGG Gene Set Enrichment Analysis	enrich_gsea_kegg
Network of Cancer Genes (NCG) Gene Set Enrichment Analysis	enrich_gsea_ncg
Reactome Gene Set Enrichment Analysis	enrich_gsea_reactome
WikiPathways Gene Set Enrichment Analysis	enrich_gsea_wp
Disease Ontology (DO) Over Representation Analysis	enrich_ora_do
GO Over Representation Analysis	enrich_ora_go
KEGG Over Representation Analysis	enrich_ora_kegg
Network of Cancer Genes (NCG) Over Representation Analysis	enrich_ora_ncg
Reactome Over Representation Analysis	enrich_ora_reactome
WikiPathways Over Representation Analysis	enrich_ora_wp

Package: glyfun 0.1.3

glyfun: Glycan-Centric Functional Enrichment Analysis

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Help Manual

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