The hand of William Shakespeare has been identified in scenes or passages in three Elizabethan plays previously believed to have been written by others, following linguistic "fingerprinting" tests and other new research.

Arden of Faversham, The Spanish Tragedy and Mucedorus will now be included in a major edition of collaborative plays bearing the Bard's name. Jonathan Bate, a renowned Shakespeare scholar, said the evidence has convinced him that specific parts within those plays must have had input from Shakespeare.

The three plays will be included in the edition which he is co-editing with other scholars in a collaboration between the Royal Shakespeare Company and Palgrave Macmillan. Plays known as the "Shakespeare Apocrypha" have long intrigued scholars, with claims and counter-claims over whether he could have written dramas beyond the 36 in the First Folio, the edition put together by his fellow actors after his death. Arguments over plays beyond the "authorised" collection have raged since the 18th century. The strengthened evidence will be outlined in the book, William Shakespeare and Others: Collaborative Plays, to be published on 28 October.

Bate, professor of English literature at Oxford University, says the issue is "perhaps the single most significant lacuna in 21st-century Shakespearean scholarship". Advanced computer-assisted analysis of every surviving play of the period has allowed the authors to go "quite a lot further than previous scholars" in establishing Shakespeare's involvement, he said, noting that it presents Shakespeare in a new light – as "reviser, rewriter and collaborator".

Arden of Faversham – which the RSC will stage in spring – is a 1590s domestic tragedy, published anonymously. It tells of a woman from Faversham, Kent, who conspires with her lover to murder her husband, seeking to "wash away this blood" in a manner reminiscent of Lady Macbeth. The book points out that rare words such as "copesmate" (companion), alongside distinctive imagery such as comparing a troubled mind to a muddied fountain, suggest Shakespeare's hand.

"It is a well-known play among aficionados," said Bate, "and there have been many arguments about who wrote it. But our new evidence is that at least one scene – a central encounter between the lovers – is by Shakespeare and that, possibly, Thomas Kyd is the author of other scenes." Kyd is best-known for The Spanish Tragedy, a 1580s revenge drama with later extra scenes which the computer testing now attributes to Shakespeare rather than his rival, Ben Jonson.

"There are some remarkable additional scenes and amazing dialogue about whether it's possible for a painter to portray grief or whether only a poet can produce a portrayal," said Bate.

There is strong circumstantial evidence that The Spanish Tragedy passed to Shakespeare's acting company and that the central character was played by his friend Richard Burbage, for whom he wrote Hamlet and King Lear.

Mucedorus is a 1590s tragi-comedy which Shakespeare's acting company revived in 1610 with extra scenes. Bate said: "At least one of those scenes is, we think, linguistically full of his fingerprints." It uses phrases unique to Shakespeare such as "worthless trunk" (also in Henry V) and "high extolment" (Hamlet) and his famous stage direction, "Exit, pursued by a bear" (The Winter's Tale).

But ultimately, is the writing worthy of Shakespeare? Bate said: "The passages in The Spanish Tragedy genuinely are. That has long been recognised."Another scholar, Stanley Wells, said "Shakespeare was both a great genius and a jobbing playwright. Taking a fresh look at plays that he may have had a hand in doesn't turn them into better plays than we thought they were, but it may well both increase our understanding of his professionalism."

Gregory Doran, the RSC's artistic director, described the new research as "fascinating", although he believes the ultimate test is when words are delivered from actors' mouths. "The plays were much more collaboratively written than we realise. We're suspicious in the theatre – but not in film or telly – of joint authorship," he said.

Commenting on Arden of Faversham, Doran said: "It is an absolutely terrific play. The complexity of the storytelling is brilliant and it does have strokes of absolute genius, so I'm very ready to accept that scholars might think there's Shakespeare's hand in it."