# Tools for Analyzing Sequencing Data with Unique Molecular Identifiers

## Documentation for package ‘umiAnalyzer’ version 1.0.0

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

## Help Pages

addMetaData | Add metaData
addUmiSample | Add UMI sample to an existing experiment object
AmpliconHeatmap | Amplicon heatmap
AmpliconPlot | Generate Amplicon plots
BarcodeFamilyHistogram | Consensus depth histograms
beta_binom | Beta binomial model
callVariants | callVariants using beta binomial distribution
createUmiExperiment | Method for creating a UMI experiment object
createUMIexperiment_Debarcer | Method for creating a UMI experiment object
createUmiSample | createUmiSample
createUMIsample_Debarcer | Method for creating a UMIsample object
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
QCplot | Generate QC plots
runUmiVisualizer | Function to run the umiVisualizer shiny app
saveConsData | Save consensus data
simsen | UMIexperiment data generated with SiMSen-Seq
timeSeriesGrid | Plot time series data
UmiCountsPlot | Plot UMI counts
UMIexperiment | UMIexperiment class
UMIexperiment-class | UMIexperiment class
UMIsample | UMIsample class
UMIsample-class | UMIsample class