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Open Source Science

https://github.com/biophys-turin/keywordtcga

Repository TCGA analysis with miRNA

https://github.com/biophys-turin/keywordtcga

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Repository TCGA analysis with miRNA

Basic Info
  • Host: GitHub
  • Owner: BioPhys-Turin
  • License: gpl-3.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 2.2 MB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Fork of fvalle1/keywordTCGA
Created almost 5 years ago · Last pushed over 4 years ago

https://github.com/BioPhys-Turin/keywordTCGA/blob/main/ 

[![DOI](https://zenodo.org/badge/DOI/10.3390/cancers14051150.svg)](https://doi.org/10.3390/cancers14051150)

# Multi-omics topic odeling for breast cancer

Notebooks and libraries for "Multi-omics Topic Modeling for Breast Cancer Classification"

# Run
You can simply create a Docker container with all dependencies installed

```bash
docker run -v $PWD:/home/jovyan/work -p 8888:8888 --rm -it --name topic_tcga docker.pkg.github.com/fvalle1/keywordTCGA/image:latest
```

then point your browser to [localhost](http://localhost:8888)

# Data
The data processed in our analysis when not available trough git can be accessed via [DataVersionControl](https://dvc.org)
```bash
dvc pull -r mydrive
```

# Tool
This paper comes with the [nsbm](https://github.com/fvalle1/nsbm/) tool available which enables the possibility of running multi omics topic modeling on many kind of data.

# License
Please see [LICENSE](LICENSE)

Owner

  • Name: Biophys Turin group
  • Login: BioPhys-Turin
  • Kind: organization
  • Email: caselle@to.infn.it
  • Location: Italy

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