Destin2: Integrative and cross-modality analysis of single-cell chromatin accessibility data.
Destin2: Integrative and cross-modality analysis of single-cell chromatin accessibility data.
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DOI：
10.3389/fgene.2023.1089936
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发表时间：
2023
影响因子：
3.7
通讯作者：
Jiang, Yuchao
中科院分区：
文献类型：
--
作者：
Guan, Peter Y. Y.;Lee, Jin Seok;Wang, Lihao;Lin, Kevin Z. Z.;Mei, Wenwen;Chen, Li;Jiang, Yuchao
关键词：
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We propose Destin2, a novel statistical and computational method for cross-modality dimension reduction, clustering, and trajectory reconstruction for single-cell ATAC-seq data. The framework integrates cellular-level epigenomic profiles from peak accessibility, motif deviation score, and pseudo-gene activity and learns a shared manifold using the multimodal input, followed by clustering and/or trajectory inference. We apply Destin2 to real scATAC-seq datasets with both discretized cell types and transient cell states and carry out benchmarking studies against existing methods based on unimodal analyses. Using cell-type labels transferred with high confidence from unmatched single-cell RNA sequencing data, we adopt four performance assessment metrics and demonstrate how Destin2 corroborates and improves upon existing methods. Using single-cell RNA and ATAC multiomic data, we further exemplify how Destin2’s cross-modality integrative analyses preserve true cell-cell similarities using the matched cell pairs as ground truths. Destin2 is compiled as a freely available R package available at https://github.com/yuchaojiang/Destin2.
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发表时间：
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期刊：
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