Deconvolution of mixed cells from spatial and/or bulk gene
expression data
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Documentation for package ‘SpatialDecon’ version 1.16.0
Help Pages
| 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 |