Welcome to the forum. I would suggest reading existing forum posts to answer some of your broad questions.
You can use any tools to analyze iNat data as you would any other biodiversity/occurrence data. There are lots of existing papers that use iNat data (there are forum threads that have some of those, eg https://forum.inaturalist.org/t/published-papers-that-use-inaturalist-data-wiki-3-2022-and-2023/34753). You can also find papers on Google Scholar or similar.
You can get iNat data from GBIF as with other biodiversity data or directly from iNat if you need some specific things.
I think you’ll need to generate a research question yourself and that specific forum feedback won’t be of much use for such general questions as you have posted. As a masters student, you should really be figuring out your question and topic yourself and then researching what specific methods could help you answer that question. If you run into trouble implementing a specific method, that might be a good thing to ask about on the forum.
Good luck!