Recent advances in genomics technologies have enabled measurements of multiple data modalities at once. While we previously were limited to measuring the transcriptome or the epigenome, we may now measure both data modalities within a single cell, or identify the precise location in situ of a cell in tissue along with their cell surface proteins, or a collection of cells in situ with their transcriptomes. As more technologies expand the multiple data modalities available within individual cells, new methods are required to better quantify and identify factors associated with disease.