Man pages for umiAnalyzer
Tools for Analyzing Sequencing Data with Unique Molecular Identifiers
| 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... |
| 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,... |
| 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-class | UMIexperiment class |
| UMIsample-class | UMIsample class |
