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 |