Unified data model
Every package speaks the same tidy grammar, letting you pass glycan-rich data seamlessly through the pipeline.
The Glycoverse Ecosystem
Build glycan knowledge with a cohesive R ecosystem
Use a coordinated family of R packages to move from raw glyco-omics data to glycan-aware insights, faster than ever before.
Structure aware
Glycan topology, motifs, and enzymatic context stay connected to your quantitative measurements.
Pluggable components
Packages can be used together or independently, suitable for any glyco-omics workflow.
Explore the workflow
End-to-end code snippets
Swipe through runnable examples that mirror the glyco-omics journey from raw measurements to pathway reconstruction.
Data Loading and Preprocessing
# Support mainstream software
exp <- read_pglyco3("results.txt")
# Automatic preprocessing
clean_exp <- auto_clean(exp)Differential Expression Analysis
# ANOVA
gly_anova(clean_exp)
# Limma
gly_limma(clean_exp)GO Enrichment
# Unified function API
go_res <- gly_enrich_go(clean_exp)
# Automatic visualization
autoplot(go_res)Motif Quantification and DEA
# Advanced motif analysis
motif_exp <- quantify_motifs(clean_exp, "Lewis X")
# Ready for statistical analysis
gly_kruskal(motif_exp)Derived Traits and DEA
# Site-specific derived traits
trait_exp <- derive_traits(clean_exp)
# Again, a smooth pipeline
gly_kruskal(trait_exp)Re-build Biosynthesis Pathway
# Any glycan structure string
glycan <- "Gal(b1-3)[GlcNAc(b1-6)]GalNAc(a1-"
# Get biosynthesis insights
rebuild_biosynthesis(glycan)Meet the packages
A coordinated toolkit for glycan discovery
Modular building blocks cover the journey from raw glyco-omics measurements to annotated glycan structures.
Entrance Packages
Get started with the glycoverse ecosystem in minutes with these two entry points.
Omics Data Analysis
Tackle glycomics data from the first import through visual communication with reproducible, shareable code.
glyexp
Organize experimental context
A tidy data framework for glycoproteomics and glycomics experimental data with experiment() container.
glyread
Import diverse formats
Read quantification results from Byonic, StrucGP, pGlyco3, Glyco-Decipher, and MSFragger.
glyclean
Automatic preprocessing
Preprocess glycomics data with normalization, missing value handling, and batch correction.
glystats
Model glycomic signatures
Statistical analysis including differential testing, PCA, clustering, and survival modeling.
glyvis
Communicate insights
Exploratory visualizations for glycomics data with autoplot() methods.
Glycan Structure Analysis
Connect biological meaning to glycan compositions, motifs, and enzyme pathways with interoperable libraries.
glyrepr
Consistent representations
Computational representations of glycan compositions and structures with IUPAC support.
glyparse
Interpret glycan strings
Parse IUPAC, WURCS, GlycoCT, and Linear Code into glycan structures.
glymotif
Find recurring motifs
Detect glycan motifs using subgraph isomorphism with curated databases.
glydet
Detect glycan patterns
Calculate site-specific derived traits like galactosylation and sialylation.
glyenzy
Trace enzymatic context
Simulate glycosylation biosynthesis and map glycans to glycosyltransferases.
glyanno
Annotate glycan hierarchy
Deduce glycan compositions and refine structures from mass or generic inputs.
glydb
Access glycan database
Query determined glycan structures from GlyTouCan with full linkage information.
glydraw
Draw SNFG cartoons
Draw beautiful SNFG (Symbol Nomenclature for Glycans) cartoons.