.call_stan_vb           Call Stan variational bayes for inference
.process_stan_vb_out    Process Stan output.
decontPro               Decontaminate using decontPro
decontX                 Contamination estimation with decontX
decontX-package         The 'decontX' package.
decontXcounts           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
