microrna-lung-cancer-associations

An association study to identify a robust miRNA biomarker signature at various stages of lung cancer.

https://github.com/jonnytran/microrna-lung-cancer-associations

Science Score: 44.0%

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CITATION.cff file
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codemeta.json file
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Scientific vocabulary similarity
Low similarity (13.2%) to scientific vocabulary

Last synced: 10 months ago · JSON representation ·

Repository

An association study to identify a robust miRNA biomarker signature at various stages of lung cancer.

Basic Info

Host: GitHub
Owner: JonnyTran
License: other
Language: Jupyter Notebook
Default Branch: master
Homepage:
Size: 11.6 MB

Statistics

Stars: 6
Watchers: 1
Forks: 0
Open Issues: 0
Releases: 0

Created over 9 years ago · Last pushed over 3 years ago

Metadata Files

Readme License Citation

README.md

MicroRNA dysregulational synergistic network

A association study between miRNA signatures and various stages in lung cancer

Citation

@article{tran2018microrna,
  title={MicroRNA dysregulational synergistic network: discovering microRNA dysregulatory modules across subtypes in non-small cell lung cancers},
  author={Tran, Nhat and Abhyankar, Vinay and Nguyen, KyTai and Weidanz, Jon and Gao, Jean},
  journal={BMC bioinformatics},
  volume={19},
  number={20},
  pages={25--36},
  year={2018},
  publisher={BioMed Central}
}

Project Organization

├── LICENSE
├── Makefile           <- Makefile with commands like `make data` or `make train`
├── README.md          <- The top-level README for developers using this project.
├── data
│   ├── external       <- Data from third party sources.
│   ├── interim        <- Intermediate data that has been transformed.
│   ├── processed      <- The final, canonical data sets for modeling.
│   └── raw            <- The original, immutable data dump.
│
├── docs               <- A default Sphinx project; see sphinx-doc.org for details
│
├── models             <- Trained and serialized models, model predictions, or model summaries
│
├── notebooks          <- Jupyter notebooks. Naming convention is a number (for ordering),
│                         the creator's initials, and a short `-` delimited description, e.g.
│                         `1.0-jqp-initial-data-exploration`.
│
├── references         <- Data dictionaries, manuals, and all other explanatory materials.
│
├── reports            <- Generated analysis as HTML, PDF, LaTeX, etc.
│   └── figures        <- Generated graphics and figures to be used in reporting
│
├── requirements.txt   <- The requirements file for reproducing the analysis environment, e.g.
│                         generated with `pip freeze > requirements.txt`
│
├── src                <- Source code for use in this project.
│   ├── __init__.py    <- Makes src a Python module
│   │
│   ├── data           <- Scripts to download or generate data
│   │   └── make_dataset.py
│   │
│   ├── features       <- Scripts to turn raw data into features for modeling
│   │   └── build_features.py
│   │
│   ├── models         <- Scripts to train models and then use trained models to make
│   │   │                 predictions
│   │   ├── predict_model.py
│   │   └── train_model.py
│   │
│   └── visualization  <- Scripts to create exploratory and results oriented visualizations
│       └── visualize.py
│
└── tox.ini            <- tox file with settings for running tox; see tox.testrun.org

Project based on the cookiecutter data science project template. #cookiecutterdatascience

Owner

Name: Nhat (Jonny) Tran
Login: JonnyTran
Kind: user

Website: jonny.bio
Twitter: Jonny_Wireless
Repositories: 41
Profile: https://github.com/JonnyTran

Graph neural networks, bioinformatics, and ML engineering for all things NLP, RNA/protein sequence learning, and knowledge graphs. Work GH: @JTran-IDM

Citation (CITATION.cff)

---
cff-version: 1.2.0
message: "Please cite our paper if you use this code in your own work."
title: "MicroRNA dysregulational synergistic network: discovering microRNA dysregulatory modules across subtypes in non-small cell lung cancers"
authors:
- family-names: "Tran"
  given-names: "Nhat C."
- family-names: "Abhyankar"
  given-names: "Vinay"
- family-names: "Nguyen"
  given-names: "KyTai"
- family-names: "Weidanz"
  given-names: "Jon"
- family-names: "Gao"
  given-names: "Jean X."
date-released: 2018-05-06
license: cc-by-4.0
url: "https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2536-0"

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