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Bus transit provides shorter-distance public transportation services, which are subject to various disability discrimination acts with various dedicated features. The Americans with Disabilities Act (ADA) requires that disabled individuals shall have equal rights to receive fare bus transit services, including fixed-route and door-to-door bus services. Most previous studies were mainly focused on policy aspects as part of the efforts of disability rights. The proper planning of demand requests from disabled individuals has been a critical issue but has gained insufficient attention. The existing methodologies in planning route for special transit buses for disabled individuals normally do not consider passengers' waiting time, lack sufficient flexibility, and have strict restrictions on the total number of served destinations. This paper proposes a four-module based methodology for the planning of bus transit, including demand information collection, demand clustering, transit bus assignment, and a linear programming-based route planning with different objective functions. Houston MetroLift bus transit service was employed as an example to illustrate the proposed method. Three scenarios during the route planning module were designed in this case study: (1) planning for pre-timed shortest distance, (2) planning for the pre-timed shortest waiting time of passengers, and (3) flexible planning. Results showed that scenario 1 obtained the shortest total travel time and the highest benefit for bus providers, scenario 2 is with the shortest average waiting time, while scenario 3 is real-time based with longer total travel time and longer waiting time. Scenarios 2 and 3 consider the special needs of disabled passengers.