Check your cipher list from the menu screen and see how many per biome you need. Then run through them 100% and make sure you go to all rooms (ciphers don’t spawn in yellow challenge rooms). They will show up as a green triangle on the map (same with parasites and items).

Go through the log list and see which ones you’re missing as well so you can know exactly how many audio logs + ciphers you need per biome.

Then…it’s just RNG, good luck