API for michaelgruenstaeudl/PACVr
Plastome Assembly Coverage Visualization
| Global functions | |
|---|---|
| .onAttach | Source code |
| .onLoad | Source code |
| Collapse.report | Source code |
| CovCalc | Source code |
| FilterByKeywords | Source code |
| GenerateIRSynteny | Source code |
| HistCol | Source code |
| PACVr | Man page |
| PACVr-package | Man page |
| PACVr.Chromosome.Ideogram.Plot | Source code Source code |
| PACVr.Gene.Connector.Plot | Source code |
| PACVr.Gene.Name.Plot | Source code |
| PACVr.Get.Start.End.Locations | Source code |
| PACVr.Histogram.Plot | Source code |
| PACVr.Ideogram.Tick.Plot | Source code |
| PACVr.compileCovStats | Source code |
| PACVr.complete | Man page Source code |
| PACVr.parseSource | Source code |
| PACVr.read.gb | Source code |
| PACVr.vizWithRCircos | Source code |
| ParseQuadripartiteStructure | Source code |
| RCircos.Env | Man page |
| RCircosInit | Source code |
| Reorganize.report | Source code |
| addLegend | Source code |
| addLowCovWin_relToRegionLen | Source code |
| annotateMissingRegions | Source code |
| boolToDeci | Source code |
| calcCovDepth | Source code |
| calcCovEvenness | Source code |
| checkIREquality | Source code |
| evennessScore | Source code |
| fillDataFrame | Source code |
| fillMissingRegions | Source code |
| filterByType | Source code |
| filterCovData | Source code |
| filterCovDataField | Source code |
| filterLogical | Source code |
| filterPosNumeric | Source code |
| filter_IR_genes | Source code |
| filter_IR_noncoding | Source code |
| filter_IR_regions | Source code |
| findIRAlignment | Source code |
| findIRDifference | Source code |
| fixGbkChar | Source code |
| fixReferences | Source code |
| getAmbigCounts | Source code |
| getCovData | Source code |
| getCovDepth | Source code |
| getCovDepths | Source code |
| getCovEvenness | Source code |
| getCovSummaries | Source code |
| getFeatureTags | Source code |
| getGbkRaw | Source code |
| getGenomeSummary | Source code |
| getIRBandRequirements | Source code |
| getIRCheckTypes | Source code |
| getLegendField | Source code |
| getLegendParams | Source code |
| getOutputTypes | Source code |
| getSpaceLength | Source code |
| getSumField2File | Source code |
| getSyntenyLineTypes | Source code |
| groupByRegionsName | Source code |
| is.pos.numeric | Source code |
| parseFeature | Source code |
| parseFeatures | Source code |
| plotAverageLines | Source code |
| plotIRLinks | Source code |
| plotMain | Source code |
| plotRegionNames | Source code |
| printCovStats | Source code |
| read.gbOnFix | Source code |
| read.gbSeqFeatures | Source code |
| read.gbSeqFeaturesAdapt | Source code |
| read.gbWithHandling | Source code |
| setLowCoverage | Source code |
| setLowCoverages | Source code |
| setPlotParams | Source code |
| stainRegions | Source code |
| updateRegionsSummary | Source code |
| validateColors | Source code |
| vizWithRCircos | Source code |
| writeCovTables | Source code |
| writeStatsTable | Source code |
| writeSumTables | Source code |
