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Directory of Indian Non-Governmental Organisations (NGO), Non-Profit Organisations (NPO), Voluntrary Organisations and Social Organisations by state. Some state entries merely describe the areas on which NGOs in there focus; others list and link to organization sites.
The Harvard Kennedy School of Government has developed a custom Google search that allows you to search across almost 700 think tanks and research centers worldwide. Think tanks are here defined as "institutions affiliated with universities, governments, advocacy groups, foundations, non-governmental organizations, and businesses that generate public policy research, analysis, and activity."