Fuente: WIPO "tomato" Methods of obtaining linked functional and sequence data for single cells, e.g., of a cellular sample, are provided. Aspects of the methods include functionally assaying partitioned single cells; visually indexing functionally-assayed, partitioned single cells using unique combinations of distinct nucleic acid-barcoded identifying particles; obtaining sequence data for the visually-indexed, functionally-assayed, partitioned single cells; and linking functional and sequence data for sequenced, visually-indexed, functionally-assayed, partitioned single cells. Also provided are compositions for practicing methods of the invention.