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Integrative analyses of single-cell transcriptome and regulome using MAESTRO.

ABSTRACT: 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.

SUBMITTER: Wang C

PROVIDER: S-EPMC7412809 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Integrative analyses of single-cell transcriptome and regulome using MAESTRO.

Wang Chenfei C Sun Dongqing D Huang Xin X Wan Changxin C Li Ziyi Z Han Ya Y Qin Qian Q Fan Jingyu J Qiu Xintao X Xie Yingtian Y Meyer Clifford A CA Brown Myles M Tang Ming M Long Henry H Liu Tao T Liu X Shirley XS

Genome biology 20200807 1

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 poten ...[more]

PMID: 32767996

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