| SpatialDecon-package | SpatialDecon: A package for estimating mixed cell type abundance in the regions of spatially-resolved gene expression studies | 
| cellcols | Default colors for the cell types in the safeTME matrix | 
| collapseCellTypes | Collapse related cell types within a deconvolution result | 
| create_profile_matrix | Create Custom Cell Profile Matrix | 
| derive_GeoMx_background | Derive background at the scale of the normalized data for GeoMx data | 
| download_profile_matrix | Download a cell profile matrix | 
| florets | Draw coxcomb plots as points in a graphics window | 
| mean.resid.sd | Genes' biological variability in immune deconvolution from TCGA. | 
| mergeTumorIntoX | Estimate a tumor-specific profile and merge it with the pre-specified cell profile matrix (X) | 
| mini_geomx_dataset | Small example GeoMx data | 
| mini_singleCell_dataset | Mini human colon single cell dataset | 
| nsclc | Large example GeoMx data | 
| reverseDecon | Reverse deconvolution | 
| runCollapseCellTypes | Run collapseCellTypes | 
| runCollapseCellTypes-method | Run collapseCellTypes | 
| runErrorModel | Apply error model to estimate technical SD from raw counts | 
| runMergeTumorIntoX | Run MergeTumorIntoX | 
| runMergeTumorIntoX-method | Run MergeTumorIntoX | 
| runReverseDecon | Run Reversedecon | 
| runReverseDecon-method | Run Reversedecon | 
| runspatialdecon | Run spatialdecon | 
| runspatialdecon-method | Run spatialdecon | 
| safeTME | SafeTME matrix | 
| safeTME.matches | Mapping from granularly-defined cell populations to broaded cell populations | 
| spatialdecon | Mixed cell deconvolution of spatiall-resolved gene expression data | 
| TIL_barplot | Barplot of abundance estimates |