They do not have a direct object, but may have an indirect object. SO if looking up run in another language, take care to find the right meaning of run in the dictionary and refer to the abbreviations vt and vi. Reflexive verbs are verbs where the action is done to oneself, common in most European languages. Here the object is the same person as the subject. In the dictionary they are listed as vr.
Relative clauses appear when two sentences are put together into one.
The relative pronoun which stops us from using the apples twice. The main clause is There are the apples. The relative clause is which I picked earlier because its meaning is relative to that of the main clause.