TY - JOUR AU - Wang, Chenfei AU - Sun, Dongqing AU - Huang, Xin AU - Wan, Changxin AU - Li, Ziyi AU - Han, Ya AU - Qin, Qian AU - Fan, Jingyu AU - Qiu, Xintao AU - Xie, Yingtian AU - Meyer, Clifford A. AU - Brown, Myles AU - Tang, Ming AU - Long, Henry AU - Liu, Tao AU - Liu, X. Shirley PY - 2020 DA - 2020/08/07 TI - Integrative analyses of single-cell transcriptome and regulome using MAESTRO JO - Genome Biology SP - 198 VL - 21 IS - 1 AB - 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 ATAC-seq (scATAC-seq) data from multiple platforms. MAESTRO provides functions for pre-processing, 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 scRNA-seq 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. SN - 1474-760X UR - https://doi.org/10.1186/s13059-020-02116-x DO - 10.1186/s13059-020-02116-x ID - Wang2020 ER -