He wrote and published on a wide range of topics in English literature, though he is best known for his works on William Shakespeare, Beaumont and Fletcher, and other figures in English Renaissance theatre.
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Cockayne's Small Poems collection of 1658 included verses to Humphrey Moseley, publisher of the 1647 Beaumont and Fletcher folio.
Here, according to Cibber, he made his reputation, and he is mentioned by John Downes as taking the parts of Alexas in John Dryden's All for Love, Pharnaces in Mithridates, king of Pontus, by Nathaniel Lee, acted in 1678, and Valentinian in the tragedy of Valentinian, adapted by the Earl of Rochester from Beaumont and Fletcher's play, and performed at Drury Lane in 1685.
Hoy edited a number of plays for modern editions, including the first five volumes in the New Cambridge Beaumont and Fletcher series, the Norton Critical Edition of Hamlet, and plays by Thomas Dekker and Philip Massinger.