# glycoTraitR <img src="man/figures/logo.png" style="float:right; height:140px;"/>
 
## Introduction
**Glycoproteomics** is a rapidly expanding field, but analyzing the LC-MS data remains a complex, multi-step process. In [the post](https://lgatto.codeberg.page/death-research-software/), Laurent emphasizes that software is a central player in scientific research. Here is his simple but powerful equation:
> **Experimental design + data + software = results**
For glycoproteomics data, advanced search engines such as Byonic, MSFragger, pGlyco3, Glyco-Decipher, and StructGP are indispensable for identifying glycopeptides. However, identification alone is not the end of the workflow.
Researchers need downstream analytical tools to: interpret glycan structural features, quantify glycan heterogeneity, compare biological groups, and extract mechanistic insight.
To address this need, we developed **glycoTraitR**, an R package that extends the analysis capability to the glycoproteomics context:
> **Software = Software (search engine) + Software (analysis tool, e.g., glycoTraitR)**
glycoTraitR is designed for users who want to go beyond simple differential analysis, extracting, summarizing, and analyzing glycan structural traits from GPSM data generated by **pGlyco3** or **Glyco-Decipher**.
It provides a streamlined workflow for:
- parsing WURCS 2.0 and pGlyco3 glycan strings
- computing composition & structural traits
- summarizing glycan–PSM trait matrices at site/protein level (`SummarizedExperiment`)
- performing differential trait analysis and visualizing trait changes
------------------------------------------------------------------------
## Download Package
``` r
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("matsui-lab/glycoTraitR")
```
## Package Workflow
``` text
pGlyco3 / Decipher GPSM
│
▼
Parse glycan strings
│
▼
Compute glycan traits (composition + structure)
│
▼
SummarizedExperiment (trait × PSM)
│
▼
Differential analysis & plots
```
------------------------------------------------------------------------
## Questions and collaboration
For questions or collaboration, feel free to contact me! Contributions are welcome!
