You haven't mentioned what you have in your inventory or what augments you have chosen.
You should try and listen to her footsteps when she is cloaked. You can easily tell the direction she is approaching from. As soon as she uncloaks, move away from her and try shooting her at the same time. I also read somewhere that you can watch the wet floor for footsteps to find out where she is. Personally, I didn't find this to be of much use.
She usually stops after that initial charge and launches an attack with her augments. If you have an EMP grenade you can disable her for a few seconds and empty your arsenal at her. If you have some kind of fast firing weapon like the heavy rifle or combat rifle or machine pistol, it really helps. You can also move in closer and launch your Typhoon Augment(if you have it) after the EMP.
If you don't have any lethal weapons on you, you can look in the lockers to the sides of the circular room. You will find some weapons and ammo. This is easier if you have cloak augment.
When she is charges and fires at you at the same time just hide, and use your hypostims or painkillers. I think you can find some in the same lockers I mentioned above.
And a bit of advice for the future bosses in the game: even if you are going for the pacifist play-through for the rest of the game, keep lethal weapons in your inventory for the boss fights at least. And EMP and Gas grenades really help in slowing them down.