The recent increase in publicly available single-cell datasets poses a significant challenge for integrative analysis. For example, multiple tissues have now been profiled across dozens of studies, representing hundreds of individuals and millions of cells. We refer to the challenge of harmonizing a broad swath (or the entirety) of publicly available single-cell datasets from a single organ as ‘community-wide’ integration. While a rich diversity of analytical methods can harmonize datasets of hundreds of thousands of cells, performing unsupervised ‘community-wide’ integration remains challenging, even when analyzing a single modality.
