Methods and systems for analysis of single cells

A method of analyzing a heterogeneous tumor biopsy from a human subject or treatment of the tumor from the human subject, comprising:

• i. dissociating the tumor biopsy into individual cells, flowing the dissociated tumor biopsy through a microfluidic metamaterial to split the flow according to particle size and randomly partition the cells into a prefabricated microwell array;
• ii. picking individual cells by expression of at least one cell surface marker from the microwell array and transferring each individual cell into a discrete location using an automated microfluidic system;
• iii. performing transcriptome analysis on at least 50 genes of the individually selected cells;
• and
• iv. identifying one or more diagnostic markers present in the tumor biopsy from transcriptome data obtained from the transcriptome analysis for the detection of cancer and determining of the cancer stage or the effectiveness of treatment of the tumor from the human subject.