I have a friend at school and she is really really cool. For some reason though, she doesn't like talking to me very much. Or so it seems, I mean we talk a lot but sometimes I say something too comfortable, and she gets all awkward and some times stop talking to me. Am i annoying her, does she like me, or does she want nothing to do with me? I'm so confused

Maybe she's confused about how she feels about you. Try asking her if you haven't already. It's worth a shot I suppose.

A friend is there no matter what.

Will she be there no matter what?

You find the answer.

Are you able to pinpoint when she becomes uncomfortable? For instance, is it when you start a talking about a certain subject or make certain gestures or look at her a certain way.

From a girl's perspective, it's not necessarily what a guy will say that will make me uncomfortable, it's typically a look he gets.

i don't think she dislikes you because you guys hang out/talk a lot, right?
maybe she likes you. or it could be that she thinks you like her and it's making her uncomfortable since she doesn't like you. either way, the best way to find out:

ASK HER