🤔 How to install ? Check the installation vignette.
🤓 How to use ? Check the website (with tutorials): audrey-onfroy.github.io/aquarius/.
Purpose
When analyzing single-cell RNA sequencing data, it is useful to develop functions. It leads to the creation of a “all_functions.R” file, which is sourced within each R file. I put all these functions in one package. Rather than sourcing all my functions in each R file, I only call the function I want to use with the aquarius::one_function notation. Creating a package forces me to write a documentation for each function and learn how to create a package.
Note that all of the functions are wrappers of functions from well-known packages. I did not develop any new or original functions or algorithms.
Use cases
aquarius has been used in:
- Onfroy et al., Hair follicle stem cell fate supports distinct clinical endotypes in Hidradenitis Suppurativa, bioRxiv 2025.05.28.656362, DOI: 10.1101/2025.05.28.656362
- Mansour, Onfroy et al., Exploring the mechanisms governing the initiation of plexiform neurofibromas using Prss56Cre,Nf1-KO mouse model at a single-cell resolution, bioRxiv 2025.07.04.662123, DOI: 10.1101/2025.07.04.662123
- Onfroy et al., Twelve tips for reproducible analysis of single-cell transcriptomics data, ACM REP ’25: Proceedings of the 3rd ACM Conference on Reproducibility and Replicability, DOI: 10.1145/3736731.3746138
Development and contribution
- Feel free to ask questions in the issues.
- The vignettes associated with CNV analysis are under development.
If you want to contribute: - fork the repository - make the improvement - ask for a pull-request
Citing
To cite this work, please use:
Audrey Onfroy,
aquarius: R package of wrappers for scRNA-Seq analysis, Zenodo, DOI: 10.5281/zenodo.15763899