https://github.com/krassowski/computational-notebooks-for-biomedical-research

NGSeminar on the use of Jupyter and R notebooks in biomedical research
https://github.com/krassowski/computational-notebooks-for-biomedical-research

biomedical jupyter-notebook jupyterlab notebook reproducible-research research rmarkdown seminar talk

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NGSeminar on the use of Jupyter and R notebooks in biomedical research

• Host: GitHub
• URL: https://github.com/krassowski/computational-notebooks-for-biomedical-research
• Owner: krassowski
• License: mit
• Created: 2020-07-15T18:00:32.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2023-01-28T12:20:09.000Z (over 2 years ago)
• Last Synced: 2025-03-26T21:03:08.586Z (about 2 months ago)
• Topics: biomedical, jupyter-notebook, jupyterlab, notebook, reproducible-research, research, rmarkdown, seminar, talk
• Language: Jupyter Notebook
• Homepage:
• Size: 8.25 MB
• Stars: 12
• Watchers: 2
• Forks: 2
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Computational notebooks for biomedical research

The slides are available as a notebook on GitHub [`Overview.ipynb`](./Overview.ipynb). Complimentary (opinionated) slides are available in other notebooks.

Run the notebooks with examples online:

- For Jupyter notebook: `Examples_Jupyter_notebook.ipynb` [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/krassowski/computational-notebooks-for-biomedical-research/master?urlpath=lab/tree/Examples_Jupyter_notebook.ipynb) (JupyterLab)

- For R Markdown: `Examples_R_Markdown.Rmd` [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/krassowski/computational-notebooks-for-biomedical-research/master?urlpath=rstudio) (RStudio)

The online environments may take some time (>10 minutes) to boot up if they are run after a fresh commit or for a first time in a while.

### Widgets screencast

For your convenience sreencasts of widgets which may be of use for biomedical researchers are embedded below:

![FASTA](media/widgets/fasta.gif)

![PDB](media/widgets/pdb.gif)

![imaging](media/widgets/imaging.gif)

![custom](media/widgets/custom.gif)

### About

This talk was given during an [NGSeminar](https://ngschool.eu/ngseminars/) on the use of Jupyter and R notebooks in biomedical research, available to [watch on YouTube](https://www.youtube.com/watch?v=eXt4MROqTtc) and later, in an improved version for the Big Data Institute training session.

### Dependencies

The Python packages used in the seminar and demonstration are listed in the [`environment.yml`](./environment.yml) file. You can install them with conda, or install specific Python requirements with pip.

The JupyterLab extensions used are listed in the `postBuild` file. You can install them by copy-pasting the line which starts with `jupyter labextension install`. In this file you will  also find the instructions on downloading the example datasets used in the presentation.