Yes! We encourage you to make this explicit on your website. Some events have used this wording:

We are trans-inclusive and welcome applications from all women.

You can add this to your FAQ, or to your event description on your event website. If you'd like to learn more about trans people, you might want to take a look at this illustrated book about gender, this comic, or any of the many other introductions to trans issues on the internet. Thanks to the PyLadies FAQ for pointing us to these excellent resources.