Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
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
Last synced: 21 days ago
JSON representation
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 (over 4 years ago)
- Default Branch: master
- Last Pushed: 2023-01-28T12:20:09.000Z (about 2 years ago)
- Last Synced: 2025-01-06T16:10:48.886Z (28 days 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
Awesome Lists containing this project
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.