https://github.com/rockerbacon/modorganizer2-linux-installer Small caveat at the moment though is that Protontricks is borked and requires a more up to date version than what's on most repos and flathub. I used the pipx install for Protontricks and that one worked though, but I think the beta branch on Flathub has an updated version now as well, which hopefully goes stable soon. Nexus is also working on a new cross platform compatible mod manager now, but that's going to be far away.

For a lot of other games r2modman + Thunderstore are also working natively on Linux. Games like Stardew Valley have a native mod manager like Stardrop.