biostudies-otherWelch JDNHGRI NIH HHSNCI NIH HHSNIGMS NIH HHS138https://www.ebi.ac.uk/biostudies/studies/S-EPMC5525279Single cell experimental techniques reveal transcriptomic and epigenetic heterogeneity among cells, but how these are related is unclear. We present MATCHER, an approach for integrating multiple types of single cell measurements. MATCHER uses manifold alignment to infer single cell multi-omic profiles from transcriptomic and epigenetic measurements performed on different cells of the same type. Using scM&T-seq and sc-GEM data, we confirm that MATCHER accurately predicts true single cell correlations between DNA methylation and gene expression without using known cell correspondences. MATCHER also reveals new insights into the dynamic interplay between the transcriptome and epigenome in single embryonic stem cells and induced pluripotent stem cells.biostudies-otherEurope PMCUnknown18(1)Genome biologyPMC5525279U01 HG007900F31 HG008912R01 HG006272T32 CA201159R01 GM118551Prins JFHartemink AJWelch JDfalseMATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics.Single cell experimental techniques reveal transcriptomic and epigenetic heterogeneity among cells, but how these are related is unclear. We present MATCHER, an approach for integrating multiple types of single cell measurements. MATCHER uses manifold alignment to infer single cell multi-omic profiles from transcriptomic and epigenetic measurements performed on different cells of the same type. Using scM&T-seq and sc-GEM data, we confirm that MATCHER accurately predicts true single cell correlations between DNA methylation and gene expression without using known cell correspondences. MATCHER also reveals new insights into the dynamic interplay between the transcriptome and epigenome in single embryonic stem cells and induced pluripotent stem cells.2017-01-01T00:00:00Z2017 Jul2019-10-28T09:53:33Z2019-03-27T02:51:31ZS-EPMC55252792873887310.5281/zenodo.81017610.1186/s13059-017-1269-0