[Q] NOT your average stuck in bootloop topic

Bear with me: Right now my nexus is stuck in a bootloop. My nexus had been partially rooted, everytime i went to download the OTA 5.0.1. update it would just take me to TWRP, and i didn't know what to do with that. So I finally tried to fully root the phone, and also use TWRP to install the OTA update. Now I'm stuck, I've tried wiping the cache/factory reset. How do I got about flashing it back to stock without losing all my data?

(apologies for the title, I thought originally that I had killed mtp and adb, but I figured out how to get them back just after posting)

Thanks!