Tools for Analyzing Sequencing Data with Unique Molecular Identifiers

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Documentation for package ‘umiAnalyzer’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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