AmpliconHeatmap         Amplicon heatmap
AmpliconPlot            Generate Amplicon plots
BarcodeFamilyHistogram
                        Consensus depth histograms
QCplot                  Generate QC plots
UMIexperiment-class     UMIexperiment class
UMIsample-class         UMIsample class
UmiCountsPlot           Plot UMI counts
addMetaData             Add metaData
addUmiSample            Add UMI sample to an existing experiment object
beta_binom              Beta binomial model
callVariants            callVariants using beta binomial distribution
createUMIexperiment_Debarcer
                        Method for creating a UMI experiment object
createUMIsample_Debarcer
                        Method for creating a UMIsample object
createUmiExperiment     Method for creating a UMI experiment object
createUmiSample         createUmiSample
download_template       Download meta data template
filterUmiObject         Method for filtering UMIexperiment and sample
                        objects
filterVariants          Filter variants based on p values or depth
findConsensusReads      Find consensus reads A function to analyze
                        consensus read tables generated with
                        parseBamFiles or a UMIexperiment object
                        containing reads.
generateVCF             Generate VCF file from UMI sample or UMI
                        experiment object
getFilteredData         Method for retrieving filtered data
getMetaData             Retrieve meta data by name.
importBedFile           Import bed file
importDesign            Import experimental design meta data such as
                        replicates, treatments, categorical variables.
mergeAssays             Merge assays
parseBamFiles           Function to parse bam files
runUmiVisualizer        Function to run the umiVisualizer shiny app
saveConsData            Save consensus data
simsen                  UMIexperiment data generated with SiMSen-Seq
timeSeriesGrid          Plot time series data
