If my doors are stuck open, how do I manually close them?
The only way to close your doors is to repair the "doors" system (appears as a vertical equals symbol). It only has to be repaired one point to allow you to close all doors. This will be very difficult to do in your situation as your crew may die of oxygen deprivation before they can make it to the door control and perform the necessary repairs. In this case you appear to be beyond all hope.
you have only one option... start a new game. You have hit the shoals with this one.
If you had money, you could upgrade your doors again to get them closed. If you had an upgraded, undamaged medbay, you could heal your guys then use the team of them to repair one bar before all of them died. If you had an undamaged pilots chair, you could jump until something either blew you up or helped you out. Sadly, none of those apply.
That's why upgrading your life support and opening only as few doors as necessary (preferably creating long, winding path for air to escape) are both useful to recover from situations like this. See below.
Experiment set-up: level 1 life support, starboard airlock open, all rooms but O2, engines and aft airlock vented. The yellow arrow shows the path of air escaping the ship.
Engaging L2 life suport allows even badly injured crew members to reach most rooms safely despite them still being open to vacuum.