| scafari-package | scafari: analyzing scDNA-seq data |
| 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 |