My personal combo is to use to Atlasssian toolbox (including JIRA, Confluence and Bitbucket). They are super complete, though a bit on the pricy side. But they offer a wide range of possibilities, and it's a great way to handle a project in general.
Now, with Github projects you also have a great tool available for handling collaboration with other developers, though it has less functionalities than JIRA !
Aside, of course Slack is a must I think (some people start to use Discord around here !). I also recommend Paw for teams, a super good tools when coming to API's.