refactor: updates of documentation and extension of unit tests

[jorainer]

• Small fixes and formatting changes in the code.
• Expand unit tests to cover additional scenarios.
• Update/restructure documentation.

[jorainer]

really big thanks for the great code and contribution @philouail !

[philouail]

Thanks so much @jorainer for polishing everything ! it looks so much better, I do have some questions in comments !

Also the checks don't pass because of the Spectra package update aha

[jorainer]

The updates in the Spectra package should become available later today or tomorrow I guess - I pushed yesterday to Bioconductor.