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keywordtcga

Repository TCGA analysis with miRNA

https://github.com/fvalle1/keywordtcga

Science Score: 67.0%

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

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

Keywords

topic-modeling
Last synced: 4 months ago · JSON representation ·

Repository

Repository TCGA analysis with miRNA

Basic Info
  • Host: GitHub
  • Owner: fvalle1
  • License: gpl-3.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage:
  • Size: 2.05 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Topics
topic-modeling
Created almost 5 years ago · Last pushed over 3 years ago
Metadata Files
Readme License Citation

README.md

DOI

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

Data

The data processed in our analysis when not available trough git can be accessed via DataVersionControl bash dvc pull -r mydrive

Tool

This paper comes with the nsbm tool available which enables the possibility of running multi omics topic modeling on many kind of data.

License

Please see LICENSE

Owner

  • Name: Filippo Valle
  • Login: fvalle1
  • Kind: user
  • Location: Turin, Italy
  • Company: @Elemento-Modular-Cloud

Chief Technology Officer of @Elemento-Modular-Cloud | Complex Systems researcher @BioPhys-Turin

Citation (CITATION.cff) 

ff-version: 1.2.0
message: "Please cite the paper below."
authors:
- family-names: "Valle"
  given-names: "Filippo"
  orcid: "https://orcid.org/0000-0003-3577-8667"
- family-names: "Osella"
  given-names: "Matteo"
  orcid: "https://orcid.org/0000-0002-4916-5434"
- family-names: "Caselle"
  given-names: "Michele"
  orcid: "https://orcid.org/0000-0001-5488-142X"
title: "Multiomics Topic Modeling for Breast Cancer Classification"
version: 1.0.0
doi: 10.3390/cancers14051150
date-released: 2021-12-23
url: "https://github.com/BioPhys-Turin/keywordTCGA"

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Dependencies

environment.yml pypi
  • cloudpickle *
  • pandas *
  • plotly *
  • seaborn *
  • sklearn *
  • topicpy *