Man pages for SpatialDecon
Deconvolution of mixed cells from spatial and/or bulk gene expression data
| algorithm2 | SpatialDecon mixed cell deconvolution algorithm |
| cellcols | Default colors for the cell types in the safeTME matrix |
| collapseCellTypes | Collapse related cell types within a deconvolution result |
| convertCellScoresToCounts | Convert abundance measurements to cell counts |
| convertCellTypes | Convert results from an arbitrary training matrix to our... |
| deconLNR | Deconvolution using logNormReg package to run linear mean... |
| derive_GeoMx_background | Derive background at the scale of the normalized data for... |
| deriveWeights | Compute gene weights |
| download_profile_matrix | Download a cell profile matrix |
| flagOutliers | Identify outlier genes in a decon result |
| florets | Draw coxcomb plots as points in a graphics window |
| mean.resid.sd | Genes' biological variability in immune deconvolution from... |
| mergeTumorIntoX | Estimate a tumor-specific profile and merge it with the... |
| mini_geomx_dataset | Example GeoMx data |
| reverseDecon | Reverse deconvolution |
| runErrorModel | Apply error model to estimate technical SD from raw counts |
| safeTME | SafeTME matrix |
| safeTME.matches | Mapping from granularly-defined cell populations to broaded... |
| spatialdecon | Mixed cell deconvolution of spatiall-resolved gene expression... |
| SpatialDecon-package | SpatialDecon: A package for computating the notorious bar... |
| tidy_X_and_Y | Function to format Y, X inputs for decon |
| TIL_barplot | Barplot of abundance estimates |
