RT Journal Article
SR Electronic
T1 scAMACE: Model-based approach to the joint analysis of single-cell data on chromatin accessibility, gene expression and methylation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.03.29.437485
DO 10.1101/2021.03.29.437485
A1 Jiaxuan Wangwu
A1 Zexuan Sun
A1 Zhixiang Lin
YR 2021
UL http://biorxiv.org/content/early/2021/03/31/2021.03.29.437485.abstract
AB The advancement in technologies and the growth of available single-cell datasets motivate integrative analysis of multiple single-cell genomic datasets. Integrative analysis of multimodal single-cell datasets combines complementary information offered by single-omic datasets and can offer deeper insights on complex biological process. Clustering methods that identify the unknown cell types are among the first few steps in the analysis of single-cell datasets, and they are important for downstream analysis built upon the identified cell types. We propose scAMACE for the integrative analysis and clustering of single-cell data on chromatin accessibility, gene expression and methylation. We demonstrate that cell types are better identified and characterized through analyzing the three data types jointly. We develop an efficient expectation-maximization (EM) algorithm to perform statistical inference, and evaluate our methods on both simulation study and real data applications. We also provide the GPU implementation of scAMACE, making it scalable to large datasets. The software and datasets are available at https://github.com/cuhklinlab/scAMACE_py (pythom implementation) and https://github.com/cuhklinlab/scAMACE (R implementation).Competing Interest StatementThe authors have declared no competing interest.