Package: glyrepr 0.14.0

Bin Fu

glyrepr: Representation for Glycan Compositions and Structures

Computational representations of glycan compositions and structures, including details such as linkages, anomers, and substituents. Supports varying levels of monosaccharide specificity (e.g., "Hex" or "Gal") and ambiguous linkages. Provides robust parsing and generation of IUPAC-condensed structure strings. Optimized for vectorized operations on glycan structures, with efficient handling of duplications. As the cornerstone of the glycoverse ecosystem, this package delivers the foundational data structures that power glycomics and glycoproteomics analysis workflows.

Authors:Bin Fu [aut, cre, cph]

glyrepr_0.14.0.tar.gz
glyrepr_0.14.0.zip(r-4.7-any)
glyrepr_0.14.0.tar.gz(r-4.7-any)glyrepr_0.14.0.tar.gz(r-4.6-any)
glyrepr_0.14.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
glyrepr/json (API)

# Install 'glyrepr' in R:
install.packages('glyrepr', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

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

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

On CRAN:

Conda:

6.56 score 15 packages 49 scripts 522 downloads 68 exports 25 dependencies

Last updated from:60909479c3. Checks:5 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK156
source / vignettesOK194
linux-release-x86_64OK155
windows-devel-x86_64OK106
wasm-releaseOK120

Exports:as_glycan_compositionas_glycan_structureavailable_monosaccharidesavailable_substituentscanonicalize_glycan_graphconvert_to_genericcount_monofill_anomer_posget_anomerget_anomer_posget_mono_typeget_structure_graphsget_structure_levelglycan_compositionglycan_structuregraph_to_iupachas_linkagesinfer_anomer_posis_glycan_compositionis_glycan_structureis_known_monosacchariden_glycan_corenew_glycan_structureo_glycan_core_1o_glycan_core_2possible_linkagesreduce_structure_levelremove_linkagesremove_substituentsseverysimapsimap_chrsimap_dblsimap_intsimap_lglsimap_structuresimap_vecsmapsmap_chrsmap_dblsmap_intsmap_lglsmap_structuresmap_uniquesmap_vecsmap2smap2_chrsmap2_dblsmap2_intsmap2_lglsmap2_structuresmap2_vecsnonespmapspmap_chrspmap_dblspmap_intspmap_lglspmap_structurespmap_vecssomestructure_edgesstructure_from_tibblesstructure_nodesstructure_to_iupacvalid_linkagesvalidate_glycan_graphvalidate_glycan_graph_vector

Dependencies:backportscheckmateclicpp11dplyrgenericsglueigraphlatticelifecyclemagrittrMatrixpillarpkgconfigpurrrR6rlangrstackdequestringistringrtibbletidyselectutf8vctrswithr

Efficient Glycan Manipulation with smap
Overview | Unique Structure Optimization | The Problem | The Solution | Memory Savings | The smap Family | Structure-Aware Mapping | The smap Toolkit | Basic Examples | Beyond Basic smap() | Performance | Additional Patterns | Working with Complex Functions | Combining Multiple Metrics | Memory-Efficient Filtering | When to Use smap Functions | Example: Custom Motif Detection | Summary | Session Information
Rendered fromsmap.Rmdusingknitr::rmarkdown

Last update: 2026-07-05
Started: 2025-09-23

Getting Started with glyrepr
Glycan Composition Vectors | Creating Glycan Composition Vectors | Two Types of Monosaccharide Names | Inspecting Glycan Composition Vectors | Manipulating Glycan Composition Vectors | Working with Tibbles | Missing Values and Names | Glycan Structure Vectors | Creating Glycan Structure Vectors | Inspecting Glycan Structure Vectors | Structure Levels | Manipulating Glycan Structure Vectors | What's Next?
Rendered fromglyrepr.Rmdusingknitr::rmarkdown

Last update: 2026-04-26
Started: 2025-09-23

Glycan Graphs: The Network Behind Glycan Structures
Glycans as Graphs | What Is Stored in Memory? | Extracting the Graph | Graph Components | Vertices | Edges | Graph-Level Attributes | Working with the Graph | Using igraph | Using smap Functions | Motif Analysis with glymotif | Summary
Rendered fromglycan-graph.Rmdusingknitr::rmarkdown

Last update: 2026-04-26
Started: 2025-09-23

Readme and manuals

Help Manual

Help pageTopics
Convert to Glycan Compositionas_glycan_composition
Convert to Glycan Structure Vectoras_glycan_structure
Get Available Monosaacharidesavailable_monosaccharides
Available Substituentsavailable_substituents
Canonicalize a Glycan Graphcanonicalize_glycan_graph
Convert Monosaccharides to Generic Typeconvert_to_generic convert_to_generic.character convert_to_generic.glyrepr_composition convert_to_generic.glyrepr_structure
Get the Number of Monosaccharidescount_mono count_mono.glyrepr_composition count_mono.glyrepr_structure
Fill Anomer Positionsfill_anomer_pos
Get the Anomeric informationget_anomer
Get Monosaccharide Typesget_mono_type get_mono_type.character get_mono_type.glyrepr_composition get_mono_type.glyrepr_structure
Access Individual Glycan Structuresget_structure_graphs
Get the Structure Resolution Levelsget_structure_level
Create a Glycan Compositionglycan_composition is_glycan_composition
Create a Glycan Structure Vectorglycan_structure is_glycan_structure
Generate IUPAC-Condensed from a Glycan Graphgraph_to_iupac
Determine if a Glycan Structure has Linkageshas_linkages
Infer Anomer Positionsget_anomer_pos infer_anomer_pos
Check if a Monosaccharide is Knownis_known_monosaccharide
Example Glycan Structuresn_glycan_core o_glycan_core_1 o_glycan_core_2
Construct a Glycan Structure Vector from Trusted Datanew_glycan_structure
Generate Possible Linkagespossible_linkages
Reduce a Glycan Structure to a Lower Resolution Levelreduce_structure_level
Remove All Linkages from a Glycanremove_linkages
Remove All Substituents from a Glycanremove_substituents
Map Functions Over Glycan Structure Vectors with Indicessimap simap_chr simap_dbl simap_int simap_lgl simap_structure simap_vec
Map Functions Over Glycan Structure Vectorssmap smap_chr smap_dbl smap_int smap_lgl smap_structure smap_vec
Test Predicates on Glycan Structure Vectorssevery smap_predicates snone ssome
Apply Function to Unique Structures Onlysmap_unique
Map Functions Over Two Glycan Structure Vectorssmap2 smap2_chr smap2_dbl smap2_int smap2_lgl smap2_structure smap2_vec
Map Functions Over Glycan Structure Vectors and Multiple Argumentsspmap spmap_chr spmap_dbl spmap_int spmap_lgl spmap_structure spmap_vec
Convert Glycan Structures to Graph Tablesstructure_edges structure_from_tibbles structure_nodes structure_tables
Convert Glycan Structure to IUPAC-like Sequencestructure_to_iupac
Check if Linkages are Validvalid_linkages
Validate a Glycan Graphvalidate_glycan_graph
Validate Compatibility Across Glycan Graphsvalidate_glycan_graph_vector