# Decontamination of single cell genomics data

## Documentation for package ‘decontX’ version 1.0.0

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

## Help Pages

decontX-package | The 'decontX' package.
.call_stan_vb | Call Stan variational bayes for inference
.process_stan_vb_out | Process Stan output.
decontPro | Decontaminate using decontPro
decontPro-method | Decontaminate using decontPro
decontX | Contamination estimation with decontX
decontX-method | Contamination estimation with decontX
decontXcounts | Get or set decontaminated counts matrix
decontXcounts-method | Get or set decontaminated counts matrix
decontXcounts<- | Get or set decontaminated counts matrix
decontXcounts<--method | Get or set decontaminated counts matrix
fastNormProp | Fast normalization for numeric matrix
fastNormPropLog | Fast normalization for numeric matrix
fastNormPropSqrt | Fast normalization for numeric matrix
nonzero | get row and column indices of none zero elements in the matrix
plotBoxByCluster | Boxplot of features grouped by cell type
plotDecontXContamination | Plots contamination on UMAP coordinates
plotDecontXMarkerExpression | Plots expression of marker genes before and after decontamination
plotDecontXMarkerPercentage | Plots percentage of cells cell types expressing markers
plotDensity | Density of each ADT, raw counts overlapped with decontaminated counts
retrieveFeatureIndex | Retrieve row index for a set of features
simulateContamination | Simulate contaminated count matrix