 If you liked
Koko ni Iru yo!
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 ...then you might like
Koe no Katachi
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In Koe no Katachi and Koko ni Iru yo! there are main characters that are school students who have difficulty communicating with the others in their class, and are subjected to bullying by classmates.
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Recommended by psychic_bear
Both stories deal with some touchy story themes as well as nice art and character designs to look at as well too.
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Recommended by Disapeared_Ghost
I Am Here and A Silent Voice are two manga series that focuses on school drama and bullying (which has bigger focus in A Silent Voice than in I Am Here, but it's still seen in both). The female main character in both of these series deals with the bullying in somewhat similar ways by not doing much at first.