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
Package: glyrepr 0.12.1
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:
glyrepr_0.12.1.tar.gz
glyrepr_0.12.1.zip(r-4.7)glyrepr_0.12.1.zip(r-4.6)glyrepr_0.12.1.zip(r-4.5)
glyrepr_0.12.1.tgz(r-4.6-any)glyrepr_0.12.1.tgz(r-4.5-any)
glyrepr_0.12.1.tar.gz(r-4.7-any)glyrepr_0.12.1.tar.gz(r-4.6-any)
glyrepr_0.12.1.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://glycoverse.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/glycoverse/glyrepr/issues
Pkgdown/docs site:https://glycoverse.github.io
Last updated from:492f3ac650 (on v0.12.1). Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 150 | ||
| source / vignettes | OK | 201 | ||
| linux-release-x86_64 | OK | 158 | ||
| macos-release-arm64 | OK | 116 | ||
| macos-oldrel-arm64 | OK | 114 | ||
| windows-devel | OK | 126 | ||
| windows-release | OK | 102 | ||
| windows-oldrel | OK | 102 | ||
| wasm-release | OK | 105 |
Exports:as_glycan_compositionas_glycan_structureavailable_monosaccharidesavailable_substituentsconvert_to_genericcount_monofill_anomer_posget_anomerget_anomer_posget_mono_typeget_structure_graphsget_structure_levelglycan_compositionglycan_structurehas_linkagesis_glycan_compositionis_glycan_structureis_known_monosacchariden_glycan_coreo_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_to_iupacvalid_linkages
Dependencies:backportscheckmateclicodetoolscpp11digestdplyrfurrrfuturegenericsglobalsglueigraphlatticelifecyclelistenvmagrittrMatrixparallellypillarpkgconfigpurrrR6rlangrstackdequestringistringrtibbletidyselectutf8vctrswithr
Efficient Glycan Manipulation with smap
Last update: 2026-04-26
Started: 2025-06-15
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
Last update: 2026-04-26
Started: 2025-06-26
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?
Last update: 2026-04-26
Started: 2025-06-15
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert to Glycan Composition | as_glycan_composition |
| Convert to Glycan Structure Vector | as_glycan_structure |
| Get Available Monosaacharides | available_monosaccharides |
| Available Substituents | available_substituents |
| Convert Monosaccharides to Generic Type | convert_to_generic convert_to_generic.character convert_to_generic.glyrepr_composition convert_to_generic.glyrepr_structure |
| Get the Number of Monosaccharides | count_mono count_mono.glyrepr_composition count_mono.glyrepr_structure |
| Fill Anomer Positions | fill_anomer_pos |
| Get the Anomeric information | get_anomer |
| Get Anomer Positions | get_anomer_pos |
| Get Monosaccharide Types | get_mono_type get_mono_type.character get_mono_type.glyrepr_composition get_mono_type.glyrepr_structure |
| Access Individual Glycan Structures | get_structure_graphs |
| Get the Structure Resolution Levels | get_structure_level |
| Create a Glycan Composition | glycan_composition is_glycan_composition |
| Create a Glycan Structure Vector | glycan_structure is_glycan_structure |
| Determine if a Glycan Structure has Linkages | has_linkages |
| Check if a Monosaccharide is Known | is_known_monosaccharide |
| Example Glycan Structures | n_glycan_core o_glycan_core_1 o_glycan_core_2 |
| Generate Possible Linkages | possible_linkages |
| Reduce a Glycan Structure to a Lower Resolution Level | reduce_structure_level |
| Remove All Linkages from a Glycan | remove_linkages |
| Remove All Substituents from a Glycan | remove_substituents |
| Map Functions Over Glycan Structure Vectors with Indices | simap simap_chr simap_dbl simap_int simap_lgl simap_structure simap_vec |
| Map Functions Over Glycan Structure Vectors | smap smap_chr smap_dbl smap_int smap_lgl smap_structure smap_vec |
| Test Predicates on Glycan Structure Vectors | severy smap_predicates snone ssome |
| Apply Function to Unique Structures Only | smap_unique |
| Map Functions Over Two Glycan Structure Vectors | smap2 smap2_chr smap2_dbl smap2_int smap2_lgl smap2_structure smap2_vec |
| Map Functions Over Glycan Structure Vectors and Multiple Arguments | spmap spmap_chr spmap_dbl spmap_int spmap_lgl spmap_structure spmap_vec |
| Convert Glycan Structure to IUPAC-like Sequence | structure_to_iupac |
| Check if Linkages are Valid | valid_linkages |