tucca-cellag/tucca-rna-seq is the Tufts University Center for Cellular Agriculture's (TUCCA) RNA-Seq workflow specifically designed for cellular agriculture projects.

This workflow was developed using the Snakemake workflow management system. tucca-rna-seq is a standardized usage Snakemake workflow that follows the best practices laid out in the Snakemake documentation (as of Snakemake v9.3) and can be found in the Snakemake Workflow Catalog.

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[!WARNING] This workflow is still under construction. Release v0.9.0 marks our first public release. v0.9.0 contains all logic to process raw paired-end RNA-Seq reads through differential expression. Currently, the workflow can generate a large number of DESeq2 result files, especially for experiments with multiple conditions and contrasts. While this is thorough, we recognize that navigating dozens of individual result files can be challenging. The centerpiece of the v1.0.0 release will be an interactive analysis toolkit that allows you to dynamically explore and visualize your results. This will include a suite of Shiny applications leveraging powerful packages like pcaExplorer, ideal, and GeneTonic to bring your data to life, as well as custom scripting to generate our favorite clusterProfiler figures. We encourage users to test this v0.9.0 release and provide feedback. Users should expect our documentation to be incomplete and continue to have major reworks until v1.0.0 is released. Please open an issue to report any bugs or suggest improvements. Additionally, feel free to contact us with any questions.

Documentation

The usage of this workflow is described in our documentation at tucca-cellag.github.io. If you've found a bug or there is a feature that we're missing (in the workflow or in our documentation) please open an issue to let us know.

Workflow Overview

Created in https://BioRender.com

Rulegraph

Created via `snakemake --rulegraph`

How do I get help?

For questions or suggestions regarding the workflow, first, check out our detailed documentation at tucca-cellag.github.io. If you can't find the answer to your question in our documentation you can try checking if someone has previously opened an issue answering your question. If you still have a question please open an issue so we can help! For any other inquiries, please contact us via email.

Citing the Workflow

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and its DOI (above if available). You should also cite the individual tools used in this workflow. See CITATIONS.md for details.

What is Cellular Agriculture? 🧬🌱

Cellular Agriculture is a cutting-edge field that harnesses biotechnology to produce agricultural products directly from cells. Unlike traditional farming, which relies on raising and harvesting whole organisms, cellular agriculture focuses on cultivating animal cells in controlled environments to create sustainable alternatives for meat, dairy, and other animal-derived products.

Why Cellular Agriculture Matters

• Sustainability 🌍: Reduces the environmental impact associated with conventional agriculture, including lower greenhouse gas emissions, reduced land and water usage, and minimized waste production.
• Ethical Considerations 🐮❤️: Offers humane alternatives by eliminating the need for animal slaughter, addressing animal welfare concerns.
• Food Security 🍽️: Enhances the ability to produce food in areas with limited agricultural resources, contributing to global food security.
• Innovation and Research 🔬: Drives advancements in biotechnology, genetics, and bioinformatics, fostering interdisciplinary collaboration and novel scientific discoveries.

Contributing

We welcome your involvement in the development of this workflow via submission of bug reports, proposing new features, engaging in discussions, or providing fixes and other code modifications. If you're interested in contributing, please consult the contributing guidelines. For all interactions within the tucca-cellag community, we ask that you observe our code of conduct.

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