There are many more tasks in NLP than what SpaCy offers even though it is a nice API. I use SpaCy near daily, but academic research goes beyond NER, dep parsing and PoS tagging.

For instance, [1] is a tool for text-to-pictograph translation system I worked on. The core engine is entirely written in Perl 5.

[1] http://picto.ccl.kuleuven.be/index_engspa.php