Integrative analyses of single-cell transcriptome and regulome using MAESTRO

Genome Biol. 2020 Aug 7;21(1):198. doi: 10.1186/s13059-020-02116-x.


We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO), a comprehensive open-source computational workflow ( ) 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.

Keywords: Cell-type annotation; Computational workflow; Integrate scRNA-seq and scATAC-seq; Predict transcriptional regulators; Single-cell ATAC-seq; Single-cell RNA-seq.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bone Marrow Cells / metabolism
  • Case-Control Studies
  • Gene Expression Regulation*
  • Humans
  • Leukemia, Lymphocytic, Chronic, B-Cell / metabolism
  • Models, Genetic*
  • Sequence Analysis, RNA
  • Single-Cell Analysis*
  • Software*
  • Transcriptome*
  • Tumor Microenvironment