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SoptSC for single cell data analysis: unsupervised inference of clustering, cell lineage, pseudotime and cell-cell communication network from scRNA-seq data.

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WangShuxiong/SoptSC

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SoptSC

Package used for the inference of clustering, cell lineage, pseudotime and cell-cell communication network from scRNA-seq data.

SoptSC

Key features of SoptSC

> 1. Estimation of the number of clusters from the single-cell data.
> 2. Identification of cell subpopulations.
> 3. Identification of DEGs for each cell subpopulation.
> 4. Inference of pseudotime in an unsupervised manner: i.e., initial cell is not required.
> 5. Inference of cell lineage and trajectory in an unsupervised manner: i.e., initial cluster is not required. 
> 6. Inference of cell-cell communication network given a group of Ligand-Receptor pairs and their downstream target genes.

Tutorials

  • Requires: MATLAB R2019 or later.
  • Click here to go through all the steps
  • Data used for each figure is deposit under folder 'Data'
  • Please refer to each M file for more detailed descriptions of the corresponding function.

Performance on clustering

Clustering

For citation, please refer to

Please feel free to contact us if you have any question: shuxionw 'at' uci 'dot' edu

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SoptSC for single cell data analysis: unsupervised inference of clustering, cell lineage, pseudotime and cell-cell communication network from scRNA-seq data.

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