Danio rerio Library, danRerLib

danRerLib has been published in Bioinformatics Advances under the title danRerLib: a python package for zebrafish transcriptomics. The full publication can be found here.

Citation

Ashley V Schwartz, Karilyn E Sant, Uduak Z George, danRerLib: a python package for zebrafish transcriptomics, Bioinformatics Advances, 2024;, vbae065, https://doi.org/10.1093/bioadv/vbae065.

Development

danRerLib has been developed by the SDSU Computational Toxicology Laboratory with primary Python code contributions from Ashley Schwartz. Karilyn E. Sant and Uduak Z. George conceived the study.

Funding

This work was supported by a National Institute of Health (National Institute of Diabetes and Digestive and Kidney Diseases) award [1R21DK134931-01 to U.Z.G and K.E.S]. Support for K.E.S. was also provided by the National Institute of Environmental Health Sciences [K01ES031640]. Support for U.Z.G was also provided by a National Science Foundation CAREER award [DMS2240155]. A.V.S. acknowledges support from the San Diego Achievement Rewards for College Scientists Foundation and the College of Sciences at San Diego State University.

Disclaimer

“Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the funding organizations.”

Description

danRerLib, short for Danio rerio library, is a comprehensive toolkit designed in Python specifically for zebrafish researchers, focusing on transcriptomics.

Documentation

The documentation for the library is currently being hosted on San Diego State University's Computational Toxicology Laboratory website. The full GitHub repository is located here.

Installation

The package requires Python>3.9 and < 3.13; we recommend Python 3.9. Please see the documentationinstallation guide for more information.

Via pip:

pip install danrerlib

Via conda:

conda install sdsu_comptox::danrerlib

Examples

• Check out our in depth tutorials on the documentation page for step-by-step instructions on how to use danRerLib to its full potential.
• You can also look at our results directory to replicate a stand-alone workflow.

Project History

This project repository was started in July 2023 by Ashley Valentina Schwartz with the first version of danRerLib being developed in September 2023. The project is maintained by Ashley Valentina Schwartz and the SDSU Computational Toxicology Laboratory. The release of danRerLib occurred in early 2024 and is an evolving repository.

Folder Descriptions

src/danrerlib/

• This folder contains the source code and database for the package.

tests/

• This folder contains tests, developed with pytest, to test the functionality of the package to maintain a stable repository.

sphinx/

• This folder contains the workable documentation for the repository including tutorials and the API reference.
• This is build using spinx documentation builder.

docs/

• This folder contains the documentation that is present on the website.
• This is a duplicate of sphinx/_build/html/.

File Map (partial)

danRerLib/
│   README.md
|   pyproject.toml
|   poetry.tock
|   Makefile
│   LICENSE
|   CONTRIBUTING.md
|   CONDUCT.md
|   CHANGELOG.md
└───src/
│   └───danRerLib
│       │   __init__.py
│       │   mapping.py
│       │   KEGG.py
│       │   GO.py
│       │   enrichment.py
│       │   enrichplots.py
│       │   utils.py
│       │   settings.py
└───tests/
└───sphinx/
└───docs/