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@MAranzazuRU Not an academic but with my former iPad Pro + Apple Pencil (first gen): I used Notes to take notes as if it was paper and it was nice. I have iCloud enabled and being able to retrieve my notes in all my devices is great.
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@MAranzazuRU (I have a new iPad Pro and my Apple Pencil isn't compatible with it. I plan to buy a new one though, haven't done it yet.)
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@MAranzazuRU When it comes to annotating papers, Zotero (I think) and Papers supports handwriting annotations (Papers is not a great iPad app to be honest)