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Organs were a type of keyboard instrument.
After the Sixth Doctor repaired his TARDIS' chameleon circuit, it took on the form of an organ for some time. The Doctor played a tune upon it, but Peri Brown insisted it wasn't the right time for such things. (TV: Attack of the Cybermen)
The Tenth Doctor amplified the noise of Southwark Cathedral's organ with his sonic screwdriver. The noise distracted Richard Lazarus who then fell from the tower and died. (TV: The Lazarus Experiment)
The Eleventh Doctor encountered a gene splicer that appeared similar to an organ and the Doctor operated it as an organ is played, using it to reverse the mutations induced by it. (COMIC: Supernature)
K9 Mark 2 and Starkey tracked her down and after she was stunned by CCPCs, Starkey played a tune he'd been humming recently on the organ, succeeding in contacting her mate, the two Aeolians then left Earth. (TV: Aeolian)