AddAdj |
Calculate the adjacency matrix given a spatial coordinate matrix |
AddParSettingFAST |
Add FAST model settings for a PRECASTObj object |
coembedding_umap |
Calculate UMAP projections for coembedding of cells and features |
coembed_plot |
Coembedding dimensional reduction plot |
CosMx_subset |
A Seurat object including spatial transcriptomics dataset from CosMx platform |
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 |
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 with structurized parameters |
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 |
get_r2_mcfadden |
Calcuate the the adjusted McFadden's pseudo R-square |
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 from FAST |
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 scRNA-seq PBMC dataset |
transferGeneNames |
Transfer gene names from one fortmat to the other format |