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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.

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8.47 score 3 stars 16 dependents 49 scripts 546 downloads

glyparse - Parsing Glycan Structure Text Representations

Provides functions to parse glycan structure text representations into 'glyrepr' glycan structures. Currently, it supports StrucGP-style, pGlyco-style, IUPAC-condensed, IUPAC-extended, IUPAC-short, IUPAC-compact, WURCS, LINUCS, Linear Code, GlycoCT, and KCF format. It also provides an automatic parser to detect the format and parse the structure string.

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6.94 score 8 dependents 28 scripts 527 downloads

glyexp - Glycoproteomics and Glycomics Experiments

Provides a tidy data framework for managing glycoproteomics and glycomics experimental data. The 'GlycomicSE' and 'GlycoproteomicSE' classes extend 'SummarizedExperiment' with validated glycomics and glycoproteomics schemas. The package provides dplyr-style data manipulation functions (filter, mutate, select, arrange, slice, join) for seamless data wrangling. As the data core of the 'glycoverse' ecosystem, it provides consistent interfaces for data exchange and analysis workflows.

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6.58 score 7 dependents 46 scripts

glydraw - Draw Beautiful Symbol Nomenclature for Glycans

A 'ggplot2'-native plotting engine for drawing reproducible beautiful Symbol Nomenclature for Glycans (SNFG) glycan cartoons from glycan structure objects or text notations, with support for batch export, structural highlighting, and deep appearance customization. It follows the SNFG specification described at <https://www.ncbi.nlm.nih.gov/glycans/snfg.html>.

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6.15 score 5 dependents 4 scripts 96 downloads

glymotif - Extract Glycan Motifs from Glycan Structures

Provides comprehensive tools for glycan motif analysis and detection in glycobioinformatics research. The package enables users to identify, count, and match glycan motifs (recurring substructures) within complex glycan structures using advanced subgraph isomorphism algorithms. It includes a curated database of known motifs from the GlycoMotif database, supports both concrete and generic monosaccharide matching, and offers flexible alignment options (core, terminal, or anywhere). Key functionalities include motif presence detection, occurrence counting, detailed node-to-node mapping, and batch analysis of multiple glycans against multiple motifs. The package seamlessly integrates with the glycoverse ecosystem, particularly 'glyrepr' and 'glyparse', making it essential for structural glycomics analysis, biomarker discovery, and understanding glycan-mediated biological processes.

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5.53 score 1 stars 4 dependents 6 scripts

glydet - Describe Glycosylation Structural Properties in a Site Specific Manner

Calculate and analyze glycosylation derived traits for site-specific glycoproteomics data. Derived traits are summary features that aggregate individual glycan abundances into biologically meaningful groups (e.g., galactosylation, sialylation, fucosylation, branching). This package provides functions to compute well-established derived traits from the literature, and features a domain-specific language for defining custom derived traits tailored to specific research needs.

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5.08 score 1 dependents 6 scripts

glyclean - Perform Preprocessing on Glycomics and Glycoproteomics Data

Provides comprehensive data preprocessing tools for glycomics and glycoproteomics experiments. The package offers both automated and manual preprocessing pipelines, including normalization (median, quantile, vsn, total area), missing value handling (filtering, imputation using various methods), batch effect correction (using ComBat and other methods), data aggregation (at peptide, glycan, or site level), and quality control functions. The automated pipeline intelligently selects appropriate methods based on data characteristics and sample size, making it easy to prepare clean, analysis-ready data for downstream statistical analysis within the glycoverse ecosystem. Works seamlessly with 'glyexp::GlycomicSE', 'glyexp::GlycoproteomicSE', and 'SummarizedExperiment::SummarizedExperiment' objects to ensure data consistency and interoperability.

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4.92 score 1 dependents 20 scripts

glystats - Statistical Analysis of Glycoproteomics and Glycomics Data

Provides a unified toolbox for bioinformatics analyses of glycomics and glycoproteomics data. Implemented methods include differential testing (t-test, Wilcoxon rank-sum test, ANOVA, Kruskal–Wallis), multivariate modeling and visualization (PCA, t-SNE, UMAP), supervised learning (PLS-DA, OPLS-DA), clustering (k-means, hierarchical, consensus clustering), network analysis (weighted gene co-expression network analysis, WGCNA), survival modeling (Cox proportional hazards), correlation analysis, and ROC/AUC evaluation. All user-facing functions follow the gly_*() naming convention to facilitate auto-completion in RStudio. Analysis functions accept 'glyexp' 'GlycomicSE', 'GlycoproteomicSE', and 'SummarizedExperiment' objects as their unified data interface.

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4.86 score 2 dependents 3 scripts

glyread - Read and process glycomics and glycoproteomics data

Provides a unified interface for reading and processing quantification results from various glycomics and glycoproteomics software tools, including Byonic (ByoLogic, pGlycoQuant), StrucGP, pGlyco3 (pGlycoQuant), Glyco-Decipher, GlyHunter, and MSFragger. The package standardizes raw data from different sources, performs peptide-spectrum match (PSM) aggregation, parses glycan compositions and structures, and converts the data into a standardized 'GlycomicSE' and 'GlycoproteomicSE' objects from the 'glyexp' package for downstream analysis within the glycoverse ecosystem.

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4.57 score 1 dependents 10 scripts

glyvis - Fast Visualization For Glycoverse

Provides a unified interface for visualizing glycomics data within the 'glycoverse' ecosystem. Implements 'autoplot()' methods for various data structures including statistical results from 'glystats', experimental data from 'glyexp', and glycan structures from 'glyrepr'. Designed for rapid data exploration and quality assessment rather than publication-quality figure generation.

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4.54 score 1 dependents

glysmith - Full-Featured Analysis Pipeline for Glycomics and Glycoproteomics

glysmith provides high-level, end-to-end workflows for glycomics and glycoproteomics data analysis within the glycoverse ecosystem. It acts as an orchestrator that integrates data cleaning, quality control, derived trait computation, motif detection, statistical testing, and visualization into unified, one-command analytical pipelines. Featuring AI-assisted pipeline generation, glysmith can intelligently translate natural language research questions into executable analysis blueprints, streamlining complex bioinformatics workflows. Built on top of the 'GlycomicSE' and 'GlycoproteomicSE' data containers and domain-knowledge-aware infrastructure provided by glyclean, glydet, glymotif, glystats, glyvis, and related packages, glysmith enables users to quickly forge polished tables, figures, and analysis reports suitable for publication. The package is designed for reproducibility and ease of use, allowing both novice and advanced users to obtain standardized and structure-aware results with minimal code while retaining full flexibility for customization.

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4.45 score 6 scripts

glyenzy - Deconstruction Glycosylation Biosynthesis

Simulates the biosynthetic process of glycosylation in silico, enabling computational analysis of glycan biosynthesis pathways. Key features include: identifying specific glycosyltransferases responsible for each glycosidic bond at the bond level; reconstructing complete biosynthetic pathways for given glycans; exploring possible transformations between two glycan structures via glycosyltransferases and glycosidases; and predicting glycans that can be synthesized from substrate structures and enzyme sets. The package supports multiple glycan types including N-glycans, O-GalNAc, O-Man, O-GlcNAc, O-Fuc, and O-Glc. As a downstream component of the glycoverse ecosystem, it integrates seamlessly with 'glyrepr', 'glyparse', and 'glymotif' to provide practical, analysis-ready insights into glycan biosynthesis for omics researchers.

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4.10 score 4 scripts

glyanno - Hierarchical Glycan Annotation

Hierarchical annotation of glycans based on molecule mass, composition, and structure. Starting from a molecule mass, glyanno calculates possible glycan compositions. Given a glycan composition, glyanno further deduces possible glycan structures. For glycan structures with generic monosaccharides (e.g., "Hex", "HexNAc"), glyanno refines them into specific types (e.g., "Glc", "Gal"). For structures lacking linkage information (e.g., "Gal(??-?)GalNAc(??-"), glyanno infers the most likely linkages (e.g., "Gal(b1-3)GalNAc(a1-").

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3.88 score 6 scripts

glycoverse - Easy Install and Load the `Glycoverse`

The 'glycoverse' is a set of packages that together form a comprehensive pipeline for glycomics and glycoproteomics data analysis. This package is designed to make it easy to install and load multiple 'glycoverse' packages in a single step.

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3.72 score 5 stars 7 scripts

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).

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3.48 score

glydb - Glycan Structure Database

Provides a comprehensive database of glycan structures from GlyTouCan, including fully determined glycan structures with complete linkage, substituent, anomer, and monosaccharide information. This database serves as a foundational resource for the glycoverse ecosystem, enabling glycan structure analysis, comparison, and research applications.

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3.41 score 1 dependents 5 scripts