# Deconvolution of mixed cells from spatial and/or bulk gene expression data

## Documentation for package ‘SpatialDecon’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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