RSA keys aren’t deprecated (apart from those with shorter key lengths, e.g. 1024 bits). What’s deprecated is the use of SHA-1, and in consequence the signature algorithms that combine SHA-1 with RSA. Instead you have to use signature algorithms that combine other hash algorithms (like SHA-2) with RSA. RSA itself, and RSA keys, remain unaffected.

Another thing that may get deprecated in the coming years is RSA 1.5 padding, requiring to use PSS padding instead. Again, that doesn’t impact RSA keys, but only the algorithm parameters used with RSA.

In the context of TLS/SSH, it just means that client and server have to negotiate the RSA-based algorithm variant they both support and both deem to be safe, using the existing RSA keys.