TriTan

TriTan implements a highly efficient triple non-negative matrix factorization algorithm for integrative analysis of single-cell multiomics data to cluster cells, identify signature features, and predict cell-type-specific regulatory networks.

Key Features:

• Efficient factorization algorithm: TriTan greatly improves computational performance compared to existing methods for integrative analysis of high-dimensional single-cell multiomics data.
• Joint factorization of three omics layers: TriTan simultaneously processes transcriptomes, epigenomes, and proteomes from the same cell through three matrix factorizations.
• Cell clustering: The factorization outputs enable clustering of cells based on integrated multiomics profiles.
• Signature feature identification: TriTan identifies signature features for each cell type from the factorization results.
• Cross-omics feature association: The method uncovers feature associations across transcriptomes, epigenomes, and proteomes.
• Regulatory network prediction: TriTan facilitates identification of domains of regulatory chromatin and prediction of cell-type-specific regulatory networks.

Scientific Applications:

• Single-cell multiomics data integration: TriTan integrates transcriptomes, epigenomes, and proteomes profiled simultaneously from the same cell to understand gene regulatory networks underlying cell states.
• Cell type identification: The tool clusters cells and identifies signature features to define cell types in heterogeneous populations.
• Chromatin domain identification: TriTan outputs facilitate identification of domains of regulatory chromatin from integrated epigenomic and transcriptomic data.
• Regulatory network inference: The method predicts cell-type-specific regulatory networks by uncovering feature associations across omics layers.
• Large-scale single-cell studies: The improved computational efficiency enables implementation in large-scale single-cell multiomics studies where existing methods are computationally prohibitive.

Methodology:

TriTan uses triple non-negative matrix factorization to jointly factorize three omics matrices. The method produces three matrix factorizations that capture patterns across transcriptomes, epigenomes, and proteomes simultaneously.