well i'm not classically trained but i'll share some of what i know
i use GraphicsGale for all my pixel art since it's free. it's a bit confusing, but once you get the hang of it it's a solid program (i just wish i knew if there were keyboard shortcuts, having to move to the toolbar and click everything can get annoying sometimes).
a good (paid) option would be Aseprite, though i've never used it so i can't give any tips for that. microsoft paint also works if you're fine with that lol. it's usually better to use software meant for pixel art unless you can figure out how to make it work on a different program
i'm not familiar with gimp personally but it doesn't seem like it's entirely meant for pixel art tbh
transparency with GraphicsGale i'm still sorta figuring out, but i know it has something to do with alpha channels. sometimes i can get it to work but sometimes it doesn't let me use transparency, idk why exactly though