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As commuters shuffled through the Lexington Avenue-53rd Street subway station on Thursday morning, Tyrone Cooper serenaded the bundled-up passengers with his usual renditions of popular tunes.

But Mr. Cooper’s performance also came with a warning: “It’s too cold to be outside right now. You can get sick and die out there.”

As a cold spell cloaked New York, with temperatures reaching only into the teens, city officials urged residents to limit their time outside. But for the homeless, options were limited.

Mr. Cooper, like countless others without shelter, sought protection in transit stations and on trains. He spent Wednesday night on the subway’s E line, a popular refuge in the winter because the train stays underground during its 50-minute trip between Queens and Lower Manhattan.