Integrative analyses of single-cell transcriptome and regulome using MAESTRO

We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO), a comprehensive open-source computational workflow (http://github.com/liulab-dfci/ MAESTRO) for the integrative analyses of single-cell RNA-seq (scRNA-seq) and ATACseq (scATAC-seq) data from multiple platforms. MAESTRO provides functions for preprocessing, alignment, quality control, expression and chromatin accessibility quantification, clustering, differential analysis, and annotation. By modeling gene regulatory potential from chromatin accessibilities at the single-cell level, MAESTRO outperforms the existing methods for integrating the cell clusters between scRNAseq and scATAC-seq. Furthermore, MAESTRO supports automatic cell-type annotation using predefined cell type marker genes and identifies driver regulators from differential scRNA-seq genes and scATAC- seq peaks.