https://github.com/amanzadi/awesome-glyco

Community-curated list of software packages and data resources for Glycoscience
https://github.com/amanzadi/awesome-glyco

List: awesome-glyco

awesome awesome-list awesome-lists bioinformatics glycan glycans glycobiology glycoprotein open-source systems-biology

Last synced: about 2 months ago
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Community-curated list of software packages and data resources for Glycoscience

• Host: GitHub
• URL: https://github.com/amanzadi/awesome-glyco
• Owner: amanzadi
• License: mit
• Created: 2024-02-05T16:10:06.000Z (10 months ago)
• Default Branch: main
• Last Pushed: 2024-03-03T20:58:00.000Z (9 months ago)
• Last Synced: 2024-09-21T18:34:34.385Z (about 2 months ago)
• Topics: awesome, awesome-list, awesome-lists, bioinformatics, glycan, glycans, glycobiology, glycoprotein, open-source, systems-biology
• Homepage:
• Size: 24.4 KB
• Stars: 3
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

Awesome Lists containing this project

README

        
# awesome-glyco 

(Still under development ... 🏗️)

Community-curated list of software packages and data resources for Glycoscience [Contributions welcome](https://github.com/amanzadi/awesome-glyco/blob/main/CONTRIBUTING.md).

This collection is inspired by [awesome-single-cell](https://github.com/seandavi/awesome-single-cell).

**Recommended** label lists my favorites -- they only reflect my personal reference and are not rigorously evaluated. Contact me if you would like other software to be added!

## Contents

- [awesome-glyco](#awesome-glyco)

  - [Contents](#contents)

  - [Software packages](#software-packages)

  - [Web portals and databases](#web-portals-and-databases)

  - [Interactive visualization and analysis](#interactive-visualization-and-analysis)

## Software packages

- [Glycowork](https://github.com/BojarLab/glycowork) - [python] - Glycowork is a Python package specifically designed to simplify glycan sequence processing and analysis.

- [CandyCrunch](https://github.com/BojarLab/CandyCrunch) - [python] - CandyCrunch is a package for predicting glycan structure from LC-MS/MS data. It contains the CandyCrunch model, along with the rest of the inference pipeline and downstream spectrum processing tools.

- [GlycoSHIELD](https://github.com/GlycoSHIELD-MD/GlycoSHIELD-MD) - [python] - GlycoSHIELD is a simple MD pipeline to generate realistic glycoprotein models.

- [GlyCONFORMER](https://github.com/IsabellGrothaus/GlyCONFORMER) - [python] - Code to generate N-glycan conformer strings based on torsion angle values.

## Web portals and databases

- [GlyCosmos](https://glycosmos.org/) - [webportal] - A web portal aiming to integrate glycosciences with the life sciences. It consists of Standards, Repositories, and Data Resources, providing information about genes, proteins, lipids, pathways, and diseases. **Recommended**

- [GlyGen](https://www.glygen.org/) - [webportal] -A data integration and dissemination project for carbohydrate and glycoconjugate-related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data.**Recommended**

- [Glyco3D](https://glyco3d.cermav.cnrs.fr/) - [webportal] - Glyco3D is a portal of databases covering the three-dimensional features of monosaccharides, disaccharides, oligosaccharides (Conformations and NMR spectra), polysaccharides, glycosyltransferases, lectins, monoclonal antibodies against carbohydrates, and glycosaminoglycan binding proteins.

- [GlycoCoO](https://github.com/glycoinfo/GlycoCoO/wiki) - [database] - Glycoconjugate Ontology (GlycoCoO) is a standard ontology for glycoconjugate data (glycoprotein/glycolipid structures, publication information, biological source information, experimental data).

- [GlycoRDF](https://github.com/glycoinfo/GlycoRDF/wiki) - [database] - GlycoRDF is a standard representation for storing Glycomics data (glycan structures, publication information, biological source information, experimental data) in RDF.

## Interactive visualization and analysis

- [GlyConnect Compozitor](https://glyconnect.expasy.org/compozitor/) - [webserver] -Visualises glycan compositions as a network of relations of shared monosaccharides Outputs interactive graphs summarising information searched in the GlyConnect database.