Spatially-Aware Cell Clustering Algorithm with Cluster
Significant Assessment
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Documentation for package ‘coFAST’ version 0.2.0
Help Pages
| AddAdj | Calculate the adjacency matrix given a spatial coordinate matrix |
| AddCluster | Find clusters for SRT data |
| Addcoord2embed | Add the spatial coordinates to the reduction slot |
| AggregationScore | Calculate the aggregation score for specific clusters |
| coembedding_umap | Calculate UMAP projections for coembedding of cells and features |
| coembed_plot | Coembedding dimensional reduction plot |
| coFAST | Cell-feature coembedding for SRT data |
| CosMx_subset | A CosMix spatial transcriptomics data |
| diagnostic.cor.eigs | Determine the dimension of low dimensional embedding |
| diagnostic.cor.eigs.default | Determine the dimension of low dimensional embedding |
| diagnostic.cor.eigs.Seurat | Determine the dimension of low dimensional embedding |
| find.signature.genes | Find the signature genes for each group of cell/spots |
| get.top.signature.dat | Obtain the top signature genes and related information |
| NCFM | Cell-feature coembedding for scRNA-seq data |
| pbmc3k_subset | A toy single-cell RNA-seq data |
| pdistance | Calculate the cell-feature distance matrix |
| top5_signatures | A dataframe including top five signature genes |