Transparent centers around the life of an invisible girl, Fiona. She was dropped on her head as a baby because nobody could see her. She was one of many children born with unique "defects" cause by their parents use of a radioactive drug. The drug has been heavily restricted, but has a huge black market following. Her brothers also have powers (flying and smells.) Her father is the leader of a crime syndicate, and he uses his children to help out in nefarious efforts. (Fiona's invisibility makes her a great spy. Once she removes her clothes, nobody can tell where she is. She can also hide things in her mouth to make them invisible.)Fiona and her mother have had enough and try to escape. She enrolls in a school in small town Arizona, and then struggles as a fish out of water. Some of her friends have powers also. All of the typical big-city girl in small town tropes apply. She makes friends with a girl in a big Catholic family and a smart boy and his brother. Fiona's brothers also appear to help her (though she thinks her "flying" brother is there to hurt her.) It is hard to keep track of all the different characters - especially the boys. Fiona struggles with her feelings towards a boy - even more so after she discovers that he can see her. Eventually they make peace and the family manages to defeat the charming father.
The book is a very "chick-lit" take on super heroes. Not much time is spent going into details about the society or the science of the story. (That is a good thing - there are so many holes in the scenario, that even spending a little time would detract from the experience.) The book provides a literal take on the figurative story of the girl that nobody can see finally finding the boy that sees her for what she is.
Anathem is a long philosophical novel. The world is just different enough from ours to make it difficult to understand what is going on. Most of the book involves conversations with "math monks". They discuss math, philosophy, theoretical physics and their interaction with the secular world. Interspersed with this philosophical discussion is a "mission" and the appearance of alien visitors. They discover that they are similar but different from the humans of their planet. Eventually people from both meet up and explore possible outcomes. In structure and length, the novel feels like a fantasy work. On content, however, it is science fiction write with clear modern day mores. There are plenty of ideas to keep for a long "geek" conversation.