SNN-Cliq is a clustering method designed for high dimensional gene expression data, e.g. single-cell transcriptome data. This method can effectively cluster individual cells based on their transcriptomes, producing clustering outputs highly in accordance with the cell type origins. SNN-Cliq utilizes the concept of shared nearest neighbor (SNN) to define similarities between data points (cells) and achieve clustering by a graph theory-based algorithm.
- Linux /Windows
- R / MatLab/ Python
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Identification of cell types from single-cell transcriptomes using a novel clustering method.
Xu C, Su Z.
Bioinformatics. 2015 Feb 11. pii: btv088.