API for JunctionSeq
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
| Global functions | |
|---|---|
| DESeq2.gt.1.14 | Source code |
| DEUresultTable | Source code |
| JS.arrowChars | Source code |
| JS.axis | Source code |
| JS.perGeneQValue | Source code |
| JS.perGeneQValueBySimulation | Source code |
| JS.perGeneQValueExact | Source code |
| JUNCTIONSEQ.DEFAULT.COLOR.LIST | Man page |
| JunctionSeqCountSet | Man page |
| JunctionSeqCountSet-class | Man page |
| JunctionSeqHTML | Source code |
| `countbinIDs<-` | Source code |
| `geneIDs<-` | Source code |
| adapted.estimateDispersionsFit | Source code |
| adapted.estimateDispersionsMAP | Source code |
| adapted.localDispersionFit | Source code |
| adapted.parametricDispersionFit | Source code |
| add.gene.name.annotation | Source code |
| advlines | Source code |
| apply2 | Source code |
| applyByDimname | Source code |
| applyByDimnameOLD | Source code |
| arrangeCoefs | Source code |
| balanceFeatures | Source code |
| build.log.scale | Source code |
| buildAllPlots | Man page Source code |
| buildAllPlotsForGene | Man page Source code |
| calc.filtered.adjusted.p | Source code |
| color2transparent | Source code |
| color2transparentVector | Source code |
| constructModelFrame | Source code |
| convertHeightToWidth | Source code |
| convertWidthToHeight | Source code |
| countTableForGene | Source code |
| countbinIDs | Source code |
| defaultColorList | Man page |
| device.limits | Source code |
| doesArrayContainDim | Source code |
| drawGene | Source code |
| drawGene.noSplices | Source code |
| drawHalfLoop | Source code |
| drawHalfLoops | Source code |
| drawPlot | Source code |
| drawTranscript | Source code |
| estimateEffectSizes | Man page Source code |
| estimateEffectSizes.BigModel | Source code |
| estimateFeatureDispersionFromRow | Source code |
| estimateJunctionSeqDispersions | Man page Source code |
| estimateJunctionSeqSizeFactors | Man page Source code |
| estimateSizeFactors | Source code |
| estimateSizeFactorsForMatrix | Source code |
| estimateUnsharedDispersions | Source code |
| estimatelog2FoldChanges | Source code |
| extractFromArray | Source code |
| extractPlottingEstimates_helper | Source code |
| f.na | Source code |
| fit.character.vector | Source code |
| fit.character.vector.helper | Source code |
| fit.title | Source code |
| fit.vert | Source code |
| fitAndArrangeCoefs | Source code |
| fitBeta | Source code |
| fitDisp | Source code |
| fitDispGrid | Source code |
| fitDispGridWrapper | Source code |
| fitDispersionFunction | Source code |
| fitDispersionFunctionHelper_SIMPLE | Source code |
| fitDispersionFunction_advancedMode | Source code |
| fitDispersionFunction_simpleMode | Source code |
| fitJunctionSeqDispersionFunction | Man page Source code |
| fixRHEL5_svg_bug | Source code |
| formatArray | Source code |
| geneCountTable | Source code |
| geneIDs | Source code |
| generate.interval.scale | Source code |
| generateAllExpressionEstimates | Source code |
| generateAllExpressionEstimates.v2 | Source code |
| get.character.dim | Source code |
| get.connection.cramp | Source code |
| get.expression.data | Source code |
| get.filtered.padjust | Source code |
| get.nested.heights | Source code |
| get.nested.heights.FALLBACK | Source code |
| get.nested.heights.advanced | Source code |
| get.nested.heights.depths | Source code |
| get.nested.heights.helper | Source code |
| get.norcounts.data | Source code |
| get.rawcounts.data | Source code |
| get.rexpr.data | Source code |
| get.sig.genes | Source code |
| getAllData | Source code |
| getAllData2 | Source code |
| getAllDataList | Source code |
| getAllJunctionSeqCountVectors | Source code |
| getAutofitTxRelativeHeight | Source code |
| getBPParam | Source code |
| getColCt | Source code |
| getEffectsForPlotting | Source code |
| getLogFoldChangeFromModel | Source code |
| getModelFit | Source code |
| getMyApply | Source code |
| getPlottingDeviceFileExtension | Source code |
| getPlottingDeviceFunc | Source code |
| getPredictedEstimates | Source code |
| getPredictedEstimatesGeneLevel | Source code |
| getTimeAndDiff | Source code |
| heatColors | Source code |
| junctionSeqColors | Man page |
| loadAndCleanJSCS | Source code |
| logConditionalLikelihood | Source code |
| make.evenly.spaced.seq | Source code |
| make.evenly.spaced.seq.minor | Source code |
| make.progress.report.fcn | Source code |
| makeAllPlotPages | Source code |
| makeAnalysisNavTable | Source code |
| makeDESeqDataSetFromJSCS | Source code |
| makeGeneLevelAxis | Source code |
| makeGeneNavTable | Source code |
| makeGeneWiseTable | Source code |
| makeNavTable | Source code |
| makePlotPage | Source code |
| makeStyleKeyTable | Source code |
| makeTablePage | Source code |
| makevstaxis | Source code |
| mapGeneNames | Source code |
| mapGeneNamesToList | Source code |
| modelFrameForGene | Source code |
| modelFrameForGene.v2 | Source code |
| newJunctionSeqCountSet | Source code |
| overmerge.list | Source code |
| plotDispEsts | Man page Source code |
| plotJunctionSeqResultsForGene | Man page Source code |
| plotMA | Man page Source code |
| plotMA.OLDVER | Source code |
| plotMA_HELPER | Source code |
| plotTranscriptsOnly | Source code |
| plotting.limits | Source code |
| readAnnotationData | Man page Source code |
| readGeneInfo | Source code |
| readJunctionSeqCounts | Man page Source code |
| repString | Source code |
| reportMem | Source code |
| reportTimeAndDiff | Source code |
| rescale.coords | Source code |
| rmDepCols | Source code |
| runJunctionSeqAnalyses | Man page Source code |
| setJunctionSeqCompiledSourcePackage | Man page Source code |
| shrink.character.vector | Source code |
| shrink.character.vector.VERT | Source code |
| simpleDeparse | Source code |
| simpleReportMem | Source code |
| strStartsWith | Source code |
| strheightSRT90 | Source code |
| subsetByGenes | Source code |
| testFeatureForDJU.fromCountVector | Source code |
| testFeatureForDJU.fromRow | Source code |
| testFeatureForDJU.fromRow.simpleNormDist | Source code |
| testForDiffUsage | Man page Source code |
| testForDiffUsage.simpleNormDist | Source code |
| timediff | Source code |
| timestamp | Source code |
| truncateAggregateGene | Source code |
| vst | Source code |
| write.fmt.table | Source code |
| write.junction.bed.file | Source code |
| write.junction.bed.file.GTFCONVERT | Source code |
| write.simple.table.gz | Source code |
| write.table.gz | Source code |
| writeCompleteResults | Man page Source code |
| writeExprBedTrack | Man page Source code |
| writeSigBedTrack | Man page Source code |
| writeSizeFactors | Man page Source code |
