From memory, Lincoln was put into a disguise (not women’s attire, like Jeff) by Pinkerton, who knew of a threat against the President-elect, and who accompanied him.
There are different accounts I've read on the incident. Some say that there was no disguise but instead Lincoln remained in a sleeping car and slept during the transit through Baltimore. Others say he was awake but not in disguise. Others say he wore a cloak to disguise his features.