API for sagrudd/nanopoRe
Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data
| Global functions | |
|---|---|
| .onAttach | Source code |
| LeftRightPlot | Man page Source code |
| RepeatMaskerGR | Man page Source code |
| RunEnrichmentAnalysis | Man page Source code |
| SVMappingCharacteristicTable | Man page Source code |
| SequenceSummaryBarcodeHistogram | Man page Source code |
| SequenceSummaryBarcodeInfoGraphic | Man page Source code |
| SequenceSummaryBarcodeTable | Man page Source code |
| SequenceSummaryBasicInfoPlot | Man page Source code |
| SequenceSummaryExecutiveSummary | Man page Source code |
| SequencingSummaryActiveChannelPlot | Man page Source code |
| SequencingSummaryBarcodeMerge | Man page Source code |
| SequencingSummaryBase50 | Man page Source code |
| SequencingSummaryChannelActivity | Man page Source code |
| SequencingSummaryCumulativeBases | Man page Source code |
| SequencingSummaryCumulativeReads | Man page Source code |
| SequencingSummaryExtractRuntime | Man page Source code |
| SequencingSummaryFlowCellID | Man page Source code |
| SequencingSummaryGetChannelMap | Source code |
| SequencingSummaryGetPlatform | Man page Source code |
| SequencingSummaryHasBarcodeInfo | Man page Source code |
| SequencingSummaryPassGauge | Man page Source code |
| SequencingSummaryReadLengthHistogram | Man page Source code |
| SequencingSummaryReadLengthQualityDensity | Man page Source code |
| SequencingSummaryReadQualityHistogram | Man page Source code |
| SequencingSummarySpeedPlot | Man page Source code |
| SequencingSummaryT50 | Man page Source code |
| SequencingSummaryTemporalThroughput | Man page Source code |
| SequencingSummaryWeightedReadLength | Man page Source code |
| Vcf2FilteredGranges | Man page Source code |
| Vcf2GRanges | Man page Source code |
| addCachedYAMLValue | Man page Source code |
| addRow | Source code |
| aggregateDepthInfo | Source code |
| aggregatedOfftarget | Source code |
| aggregatedOntarget | Source code |
| bamMineUniverse | Source code |
| bamSummarise | Man page Source code |
| bamSummariseByChr | Man page Source code |
| bamSummaryToCoverage | Man page Source code |
| barcodeSeqSummary | Source code |
| buildPositionMap | Man page Source code |
| cachedYAMLToYAML | Man page Source code |
| chromosomeMappingSummary | Man page Source code |
| cigarQ2Op | Man page Source code |
| cigarQ2R | Man page Source code |
| cigarR2Op | Man page Source code |
| cigarR2Q | Man page Source code |
| cleanReferenceGenome | Man page Source code |
| collateMappingCharacteristics | Source code |
| convert_from_inches | Source code |
| convert_to_inches | Source code |
| default_device | Source code |
| enrichmentCoverageTypeOverChromosomes | Man page Source code |
| enrichmentExecutiveSummary | Man page Source code |
| enrichmentGetTargetList | Man page Source code |
| enrichmentMappingByGenomicSegment | Man page Source code |
| enrichmentMultiGeneCoveragePanel | Man page Source code |
| enrichmentOffTargetKaryogram | Man page Source code |
| enrichmentOffTargetTable | Man page Source code |
| enrichmentSingleTargetPlot | Man page Source code |
| enrichmentStrandedTargetPlot | Man page Source code |
| enrichmentTargetPerformanceTable | Man page Source code |
| enrichmentWriteExcelOffTarget | Man page Source code |
| enrichmentWriteExcelOnTarget | Man page Source code |
| extract5mC | Man page Source code |
| extract5mCProbabilities | Man page Source code |
| extractH5Modstemplate | Source code |
| extractMethylatedBases | Man page Source code |
| extractModifiedBasesFromFast5 | Source code |
| fast5parseLegend | Source code |
| fastqCheckup | Man page Source code |
| fastqValidator | Man page Source code |
| fixFastq | Man page Source code |
| getBAMReadCoverageStats | Source code |
| getBAMReadLengthStats | Source code |
| getBAMReadMappingStats | Source code |
| getBAMReadNucleotideStats | Source code |
| getBAMReadQualityStats | Source code |
| getBinAssignments | Source code |
| getBinBreaks | Source code |
| getCachedFileObject | Source code |
| getCachedObject | Source code |
| getCachedYAMLFields | Man page Source code |
| getCachedYAMLValue | Man page Source code |
| getChromosomeIds | Man page Source code |
| getChromosomeSequence | Man page Source code |
| getEnvironment | Source code |
| getFastqBases | Man page Source code |
| getFastqCount | Man page Source code |
| getFastqPlusErrorCount | Man page Source code |
| getFlongleChannelMap | Man page Source code |
| getGitDescription | Man page Source code |
| getMalformedFastqHeaderCount | Man page Source code |
| getMinIONChannelMap | Man page Source code |
| getONTlogo | Source code |
| getOutputFormat | Man page Source code |
| getPlotDimensions | Man page Source code |
| getPromethIONChannelMap | Man page Source code |
| getReadFlags | Source code |
| getReferenceGenome | Man page Source code |
| getReferenceGenomeGR | Man page Source code |
| getRpath | Man page Source code |
| getSeqLengths | Man page Source code |
| getSequenceQualityMismatchCount | Man page Source code |
| getSkippedLineCount | Man page Source code |
| getStartStrand | Source code |
| getStringSetId | Man page Source code |
| getTemporalDataset | Source code |
| getZeroLengthSequenceCount | Man page Source code |
| ggbiosave | Man page Source code |
| ggplot2handler | Source code |
| ggplot2save | Source code |
| handleCompression | Source code |
| handleSeqSumCache | Source code |
| harvestUnmappedQuals | Source code |
| hasCachedObject | Source code |
| hasCachedYAMLField | Man page Source code |
| importConfigYAML | Man page Source code |
| importEnrichmentResults | Man page Source code |
| importSequencingSummary | Man page Source code |
| infoGraphicPlot3 | Man page Source code |
| infoGraphicPlot4 | Man page Source code |
| infoGraphicPlot5 | Man page Source code |
| init | Man page Source code |
| isEnrichmentAnalysisComplete | Man page Source code |
| isInitialised | Man page Source code |
| lcalc | Man page Source code |
| listCachedObjects | Man page Source code |
| listOutputFormat | Man page Source code |
| loadMethylationBamFile | Man page Source code |
| loadReferenceGenome | Man page Source code |
| mapUniverseTypes | Source code |
| md5sum | Man page Source code |
| nanopoRe | Man page |
| nanopoRe-package | Man page |
| ncalc | Man page Source code |
| parallelBamSummarise | Man page Source code |
| parseEnrichmentBam | Source code |
| parseGenomeCoordinates | Source code |
| phredmean | Man page Source code |
| plotAlignmentAccuracy | Man page Source code |
| plotAlignmentIdentity | Man page Source code |
| plotDepthOfCoverageMegablock | Man page Source code |
| plotOverallCovHistogram | Man page Source code |
| processBamChunk | Source code |
| qualToMeanQ | Man page Source code |
| refineBarcodes | Source code |
| roundUpNice | Source code |
| selectEnvironment | Source code |
| setCachedObject | Source code |
| setCachedYAMLValue | Man page Source code |
| setLogFile | Man page Source code |
| setOutputFormat | Man page Source code |
| setPlotDimensions | Man page Source code |
| setReferenceGenome | Man page Source code |
| setRpath | Man page Source code |
| snifflesKaryogram | Man page Source code |
| svLengthDistribution | Man page Source code |
| testBam | Man page Source code |
| unsetLog | Man page Source code |
| writeTargetsToFile | Source code |
