Man pages for ProFAST
Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction
| AddAdj | Calculate the adjacency matrix given a spatial coordinate... |
| AddParSettingFAST | Add FAST model settings for a PRECASTObj object |
| coembedding_umap | Calculate UMAP projections for coembedding of cells and... |
| coembed_plot | Coembedding dimensional reduction plot |
| CosMx_subset | A Seurat object including spatial transcriptomics dataset... |
| diagnostic.cor.eigs | Determine the dimension of low dimensional embedding |
| FAST | Run FAST model for a PRECASTObj object |
| FAST_run | (Varitional) ICM-EM algorithm for implementing FAST model |
| FAST_single | Fit FAST model for single-section SRT data |
| FAST_structure | (Varitional) ICM-EM algorithm for implementing FAST model... |
| find.signature.genes | Find the signature genes for each group of cell/spots |
| get_r2_mcfadden | Calcuate the the adjusted McFadden's pseudo R-square |
| get.top.signature.dat | Obtain the top signature genes and related information |
| IntegrateSRTData | Integrate multiple SRT data into a Seurat object |
| iscmeb_run | Fit an iSC-MEB model using specified multi-section embeddings |
| model_set_FAST | Set parameters for FAST model |
| NCFM | Cell-feature coembedding for scRNA-seq data |
| NCFM_fast | Cell-feature coembedding for SRT data |
| pbmc3k_subset | A Seurat object including scRNA-seq PBMC dataset |
| pdistance | Calculate the cell-feature distance matrix |
| RunHarmonyLouvain | Embedding alignment and clustering based on the embeddings... |
| RuniSCMEB | Fit an iSC-MEB model using the embeddings from FAST |
| SelectHKgenes | Select housekeeping genes |
| top5_signatures | A data.frame object including top five signature genes in... |
| transferGeneNames | Transfer gene names from one fortmat to the other format |
