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

---

Documentation for package ‘SpatialDecon’ version 1.4.3

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

Help Pages

SpatialDecon-package	SpatialDecon: A package for computating the notorious bar statistic.
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	Collapse related cell types within a deconvolution result
runErrorModel	Apply error model to estimate technical SD from raw counts
runMergeTumorIntoX	Run MergeTumorIntoX
runMergeTumorIntoX-method	Run mergeTumorIntoX on a NanostringGeomxSet object
runReverseDecon	Run Reversedecon
runReverseDecon-method	Run reversedecon on a NanostringGeomxSet object
runspatialdecon	Run spatialdecon
runspatialdecon-method	Run spatialdecon on a NanostringGeomxSet object
runspatialdecon-method	Run spatialdecon on a Seurat object
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