https://github.com/sysbiochalmers/gagome-mced
https://github.com/sysbiochalmers/gagome-mced
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/sysbiochalmers/gagome-mced
- Owner: SysBioChalmers
- License: mit
- Created: 2022-09-23T11:49:29.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2022-12-06T09:17:58.000Z (over 3 years ago)
- Last Synced: 2025-01-30T22:51:18.537Z (over 1 year ago)
- Language: HTML
- Size: 1.11 MB
- Stars: 1
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# `GAGome-MCED`
## 🔬 Description
This repository contains code and example data sets for the publication "Noninvasive detection of any-stage cancer using free glycosaminoglycans".
Both a synthetic data set with standardized GAGome values and the code for the development of free GAGome MCED scores are available in the subfolders.
## 💻 Installation and usage
Run the Rmarkdown file Projpred_synth.Rmd in order to produce a model for predicting the probability of cancer using plasma and urine GAGomes as input data. A pre-knitted HTML report is also available if you are not interested in re-running the code yourself.
https://sysbiochalmers.github.io/GAGome-MCED/projpred_synth.html
## 📖 Publication
The free GAGome MCED scores are used in the publication below:
```
Noninvasive detection of any-stage cancer using free glycosaminoglycans
Sinisa Bratulic, Angelo Limeta, Saeed Dabestani, Helgi Birgisson, Gunilla Enblad, Karin Stålberg,
Göran Hesselager, Michael Häggman,Martin Höglund, Oscar E Simonson, Peter Stålberg, Henrik Lindman,
Anna BÃ¥ng-Rudenstam, Matias Ekstrand, Gunjan Kumar, Ilaria Cavarretta,Massimo Alfano, Francesco Pellegrino,
Thomas Mandel-Clausen, Ali Salanti, Francesca Maccari, Fabio Galeotti, Nicola Volpi, Mads Daugaard,
Mattias Belting, Sven Lundstam, Ulrika Stierner, Jan Nyman, Bengt Bergman, Per-Henrik Edqvist, Max Levin,
Andrea Salonia, Henrik Kjölhede, Eric Jonasch, Jens Nielsen, Francesco Gatto
Manuscript doi: 10.1073/pnas.2115328119
Manuscript link: https://www.pnas.org/doi/10.1073/pnas.2115328119
```
## 👋 Contact
Please reach out to our email with any comments, questions or concerns:
[Sinisa Bratulic](mailto:bratulic@chalmers.se)
[Angelo Limeta](mailto:angelol@chalmers.se)