to write in a secret code [encode, encrypt]

Hi. I could use a little help. I would like to know if there's a verb in English that means "to write in code", i.e. using a code to disguise the contents of the communication.

For example, I read somewhere: "Francis Walsingham intercepted and deciphered Mary Stuart's coded letters"

So, could I say: "Mary Stuart coded her letters" ?

What about "to cipher"? (since the opposite operation is "to decipher") Can this verb be used in the sense of writing in code?

Thanks in advance.
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