When analyzing single-cell RNA sequencing data, one develops some useful functions to avoid doing of lot of copy-pasting. Then, one builds a file “all_functions.R” which is sourced within each R file.
I put all these functions in one package ! Instead of sourcing all my functions in each R file, I only call the one I want to use with the aquarius::one_function notation. Writing a package forces me to make a clean documentation for each function, learn how to make a package, etc.
Note that all functions are wrappers of functions from well-known packages. I did not develop new original functions / algorithms.
Make aquarius re-usable
This package is in a public repository to enable the traceability of the published work. It is not supposed to be re-used by others because there are no support nor documentation yet.
This is my to-do list:
- ✅ sort the functions: discard useless, document the new ones
- ✅ ensure compatibility with R version 4, Seurat version 5: globally with latest version of the dependencies
- 🟠 make nice vignettes to illustrate the use and purpose of each (all !) function
- ⭕ add the v1.0.0 tag on the repository
- ⭕ make the new version of the software container from this tag
- ⭕ add a DOI to this repository (because the container has already one)
In a word, make aquarius readable and re-usable 😅
🚧 The site is under development, particularly, the vignettes.
audrey-onfroy.github.io/aquarius/Installation
Check the installation vignette.