https://github.com/bbglab/hartwig_biomarkers
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (5.4%) to scientific vocabulary
Last synced: 6 months ago
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JSON representation
Repository
Basic Info
- Host: GitHub
- Owner: bbglab
- Language: Jupyter Notebook
- Default Branch: main
- Size: 628 KB
Statistics
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Created almost 4 years ago
· Last pushed over 1 year ago
Metadata Files
Readme
README.md
Hartwig Biomarkers
Goal of Repository
- Clean and organize the Hartwig Medical Foundation data request files into a single dataframe.
- See Hartwig Medical Foundation: https://www.hartwigmedicalfoundation.nl/en/
Organization
Overview * For each file type, a pipeline computes and organizes features across all samples. * Output from each pipeline are then joined by their sample ids.
Prerequisites to Run
Hartwig Data Request Approval
- Data request: https://www.hartwigmedicalfoundation.nl/en/data/data-access-request/
- PURPLE, ISOFOX, and clinical data output.
Source and reference data
- Run and tested on Hartwig data request files shared on August 9, 2022.
- Source directory locations need to be specified in missioncontrol/treasuremap.*.
QMap and conda environments
- Jobs are submitted with the QMap tool from the bbglab: https://github.com/bbglab/qmap
- QMap tool calls two conda environments, stored in conda_env folder.
Run the pipeline
- From the root directory:
$ python run.py
Owner
- Name: BBGLab - Barcelona Biomedical Genomics Lab
- Login: bbglab
- Kind: organization
- Email: bbglab@irbbarcelona.org
- Location: Barcelona
- Website: http://bbglab.irbbarcelona.org
- Repositories: 16
- Profile: https://github.com/bbglab