annotateAmplicons       Function: annotateAmplicons This function takes
                        a SingleCellExperiment object as input and
                        annotates the stored amplicons.
annotateVariants        Function: annotateVariants This function takes
                        a SingleCellExperiment object as input and
                        performs variant annotation.
clusterVariantSelection
                        Function: clusterVariantSelection This function
                        takes selected variants and performs clustering
                        on them.
filterVariants          Function: filterVariants -------- This function
                        takes a SingleCellExperiment object as input
                        and performs variant filtering
h5ToSce                 Function: h5ToSce This function takes the path
                        of an h5 file and reads this into an object of
                        the SingleCellExperiment class.
launchScafariShiny      Launch Scafari Shiny Application
logLogPlot              Plot a log-log plot for read counts
normalizeReadCounts     This function normalizes the read counts
                        contained within a 'SingleCellExperiment'
                        object.
plotAmpliconDistribution
                        Plot Distribution of Amplicons
plotClusterGenotype     Plot Genotype Clusters
plotClusterVAF          plot Cluster VAF This function generates a plot
                        to visualize variant allele frequency (VAF) in
                        clusters based on selected variants of
                        interest.
plotClusterVAFMap       plot Cluster VAF Map This function generates a
                        plot to visualize variant allele frequency
                        (VAF) in clusters based on selected variants of
                        interest with clusters in the background.
plotElbow               This function takes a SingleCellExperiment
                        object and variants of interest as input and
                        plots an elbow plot to perform k-means later.
plotGenotypequalityPerGenotype
                        Plot Genotype Quality per Genotype
plotNormalizedReadCounts
                        Plot normalized read counts
plotPanelUniformity     Plot Panel Uniformity
plotVariantHeatmap      Plot Variant Heatmap
scafari                 scafari: analyzing scDNA-seq data
