The emerging diversity of single-cell RNA-seq datasets allows for the full transcriptional characterization of cell types across a wide variety of biological and clinical conditions. However, it is challenging to analyze them together, particularly when datasets are assayed with different technologies, because biological and technical differences are interspersed. We present Harmony (https://github.com/immunogenomics/harmony), an algorithm that projects cells into a shared embedding in which cells group by cell type rather than dataset-specific conditions. Harmony simultaneously accounts for multiple experimental and biological factors. In six analyses, we demonstrate the superior performance of Harmony to previously published algorithms while requiring fewer computational resources. Harmony enables the integration of ~106 cells on a personal computer. We apply Harmony to peripheral blood mononuclear cells from datasets with large experimental differences, five studies of pancreatic islet cells, mouse embryogenesis datasets and the integration of scRNA-seq with spatial transcriptomics data.
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All data analyzed in this article are publicly available through online sources. We included links to all data sources in Supplementary Table 8.
Harmony and LISI are available as R packages on https://github.com/immunogenomics/harmony and https://github.com/immunogenomics/lisi. Scripts to reproduce results of the primary analyses will be made available on https://github.com/immunogenomics/harmony2019. Additionally, vignettes are included as Supplementary Notes. Supplementary Note 1 provides a detailed walkthrough of Harmony, connecting theoretical algorithm components to their code implementations. Supplementary Note 2 demonstrates the LISI metric and how to evaluate its statistical significance. Supplementary Note 1 uses Harmony with simulated datasets.
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This work was supported in part by funding from the National Institutes of Health (grant nos. UH2AR067677 and U19AI111224 and no. 1R01AR063759 (to S.R.) and T32 AR007530-31 (to I.K.)). We thank members of the Raychaudhuri and Brenner labs for comments and discussion. I.K. and K.W. were funded as part of a collaborative research agreement with F. Hoffmann-La Roche Ltd (Basel, Switzerland), to S.R. and M.B.B.
I.K. does paid bioinformatics consulting through Brilyant LLC.
Peer review information Nicole Rusk was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Figs. 1–19.
Harmony R package. Software to perform Harmony integration analysis.
LISI R package. Software to compute the Local Inverse Simpson’s Index.
Jurkat LISI, Time benchmark, Memory Benchmark, HCA LISI, PBMC LISI, Inhibitory, Excitatory, Data Sources.
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Korsunsky, I., Millard, N., Fan, J. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat Methods 16, 1289–1296 (2019). https://doi.org/10.1038/s41592-019-0619-0
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