https://github.com/greenelab/circadian-clock-modulators
Network analysis of hits from a screen of circadian clock modulating compounds
https://github.com/greenelab/circadian-clock-modulators
circadian-medicine circadian-rhythm screen
Last synced: 2 months ago
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Network analysis of hits from a screen of circadian clock modulating compounds
- Host: GitHub
- URL: https://github.com/greenelab/circadian-clock-modulators
- Owner: greenelab
- License: other
- Created: 2020-04-06T21:26:56.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2022-12-08T09:50:05.000Z (almost 3 years ago)
- Last Synced: 2025-05-23T00:26:44.538Z (5 months ago)
- Topics: circadian-medicine, circadian-rhythm, screen
- Language: Jupyter Notebook
- Homepage:
- Size: 8.98 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 10
-
Metadata Files:
- Readme: readme.md
- License: license-bsd.md
Awesome Lists containing this project
README
# Circadian Clock Modulators
Analyzing circadian clock modulators.
## References
Figshare datasets by Tamai et al are stored in the [`data/tamai-screen`](data/tamai-screen) directory.
They were downloaded from figshare at the locations listed below, where they are available under a [CC0 License](https://creativecommons.org/publicdomain/zero/1.0/).
1. **Identification of circadian clock modulators from existing drugs**
T Katherine Tamai, Yusuke Nakane, Wataru Ota, Akane Kobayashi, Masateru Ishiguro, Naoya Kadofusa, Keisuke Ikegami, Kazuhiro Yagita, Yasufumi Shigeyoshi, Masaki Sudo, … Takashi Yoshimura
*EMBO Molecular Medicine* (2018-04-17)
DOI: [10.15252/emmm.201708724](https://doi.org/10.15252/emmm.201708724) · PMID: [29666146](https://www.ncbi.nlm.nih.gov/pubmed/29666146) · PMCID: [PMC5938619](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5938619)
2. **FDA\_Tamai et al\_Identification of circadian clock modulators from existing drugs**
Kathy Tamai, Yusuke Nakane, Takashi Yoshimura
*figshare* (2020)
DOI: [10.6084/m9.figshare.11608485.v2](https://doi.org/10.6084/m9.figshare.11608485.v2)
3. **IDC\_Tamai et al\_Identification of circadian clock modulators from existing drugs**
Kathy Tamai, Takashi Yoshimura, Yusuke Nakane
*figshare* (2020)
DOI: [10.6084/m9.figshare.11626014.v2](https://doi.org/10.6084/m9.figshare.11626014.v2)
## Environment
This repository uses Pipenv to manage its environment.
See [this post](https://towardsdatascience.com/how-to-use-pipenv-with-jupyter-and-vscode-ae0e970df486) for information on using Pipenv with notebooks and vscode.
Here are some useful commands to run from the repository's root directory:
```shell
# if conda is installed, it might help to deactivate a conda env first
conda deactivate
# install the virtual environment
pipenv install
# activate a terminal shell with this environment
pipenv shell
# start the jupyter notebook
pipenv run jupyter notebook
# add the "pandas" package to the environment (already done)
pipenv install pandas
```
## License
All original work in this repository is released under a [CC0 License](https://creativecommons.org/publicdomain/zero/1.0/).
All code in this repository is also released under a BSD-2-Clause Plus Patent License as provided in [`license-bsd.md`](license-bsd.md).