Dear networkcommoners,

I am submitting this new pull request to address the feedback provided in PR #62.

As suggested by @deeenes (btw thanks a lot for the refactoring), I have created a dedicated vignette for SignalingProfiler, with two illustrative use cases:

• One-layer network construction: this example uses networkcommons PANACEA dataset, focusing on a protein list composed exclusively of transcription factors;
• Three-layers network construction: this utilizes a more diverse protein list (including TFs, kinases, and phosphatases) derived from a dataset used in SignalingProfiler benchmarking, based on the work by Olsen et al.. For this vignette to function, I kindly request this dataset be made available on your server.

During testing, I encountered an issue with the refactored mf_classifier function in SignalingProfiler, which wasn't correctly importing the table on my side. Hence, I wasn't really able to check the vignette results.
I hope that the two use cases in the SignalingProfiler vignette can serve as useful unit tests.

Additionally, this PR includes:

• Aligment of the SignalingProfiler image and its description with the corresponding content in the paper;
• Correction of Livia Perfetto email address :)

Thank you all for the feedback and ongoing support.
Please don’t hesitate to reach out if you have any questions or suggestions.

Cheers,
Veronica and PerfettoLab