babel-exclude-ignore

By default babel ignores evertying in node_modules. This module allows to include folders from node_modules in babel transform.

var excludeIgnore = require('babel-exclude-ignore')
require('babel-core/register')({
  ignore: excludeIgnore(["my-module"])
})
// note that it will still ignore nested `/my-modules/node_modules/**` files

Also you can use it as a plugin