proteomicsbiomarkerrepco
Science Score: 44.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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○Scientific vocabulary similarity
Low similarity (14.0%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: FloorzUU
- License: mit
- Language: R
- Default Branch: main
- Size: 68.4 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
ProteomicsBiomarkerRepCo
This repository includes all code written to ensable a report for my Major Research Internship. Which aims to identify all potential biomarkers for MACE within three years after surgery which an OLINK Explore plasma protein dataset.
installation
--- detail installation and dependency requirements ---
Usage
In the main project file you can find scripts that do statistical testing anf further analysis for the large OLINK protein dataset. The testing was predominantly done for MACE, but tests were also performed for the transcriptome-defined clusters (Michals clusters) and the symptoms.
In file: MainProject/ExecuteAnalysis all other scripts are called and run such that only the desired outputs are saved in the workspace, plot viewer, printed of saved in a designated results file on the computer.
Each other script in this folder has a prefix with a description of what kind of analysis is performed within the script, it requires input and resulting output.
In the side projects folder, some stored scripts which were not covered in the report (Admittedly symptoms and clusters aren't either). But were still part of the internship. All still using proteomics data as a basis. scripts in it cover topics like: Associations with methylation-based age, macrophages, a replicated pipeline of a previously published paper and machine learning patterns for those previously mentioned clusters.
Support
In case of issues and/or questions running this code please contact: f.b.h.vanderzalm@umcutrecht.nl
Roadmap
In future updates code will be resturctured to include more functions
Contributing
Pull request are welcome. For major changes, please open an issue first to discuss what you would like to change.
Licence
Author and acknowledgements
Floor van der Zalm with acknowledgements of the contributions of my supervisor throughout this project; Michal Mokry.
Owner
- Login: FloorzUU
- Kind: user
- Repositories: 1
- Profile: https://github.com/FloorzUU
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
title: "My Research Software"
authors:
- family-names: Druskat
given-names: Stephan
orcid: https://orcid.org/1234-5678-9101-1121
version: 2.0.4
date-released: 2021-08-11
doi: 10.5281/zenodo.1234
license: Apache-2.0
repository-code: "https://github.com/citation-file-format/my-research-software"
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