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Visit the 511.org website for information on all public transit authorities in the San Francisco Bay Area, including schedules, time tables, and transit rules, etc.  This includes almost all publicly subsidized ferry services, buses, and trains.  Their website also has a destination/starting point calculator that will tell you the cheapest or the fastest way to use publicly subsidized transportation to travel within the SF Bay Area on a given date or beginning at a specific time.
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