Yes! You can enable the feature in Admin > Invoice Preferences and add Deposit items to your Inventory to start collecting these with ease.
There is a Take Deposit button on the ticket, that with just a click creates an invoice and triggers a credit to show up on the following invoice you make for that customer.
Here is a screenshot tour;
1. Click the new Take Deposit button
2. The first time you'll need to create an Inventory item like so;
3. Then that Take Deposit button will ask you to select which Deposit amount/name you want to charge them;
4. Accept the money, then you'll see on the Ticket - Charges a pending credit for the deposit amount
5. Next time you make an invoice from this Ticket, that Deposit credit will automatically show as a line item - just as expected
We also have Variable Amount Deposits - just setup a Deposit product with the price set to 0.00
Then on the Take Deposit screen, you can key in any amount you want: