API for jakeyeung/Circadian4Cseq
| Global functions | |
|---|---|
| AddCyclixTo4CSeq | Source code |
| AddDf | Source code |
| AddLR | Source code |
| AddRhythmicColumns | Source code |
| AddToEnviron | Source code |
| Annotate4CSeqWithCyclix | Source code |
| AnnotateDat | Source code |
| AnnotateLeftRightTrans | Source code |
| AnnotatePseudogenes | Source code |
| AnnotateTranscriptLength | Source code |
| AppendGeneID | Source code |
| AssayToBed | Source code |
| Attribute2Gene | Source code |
| BICFromLmFit | Source code |
| BICWeight | Source code |
| CalculatePeriodogramLong | Source code |
| CapitalizeFirstLetter | Source code |
| Center | Source code |
| ChowStatistic | Source code |
| ChunkDatGenesToFile | Source code |
| CoefToModelName | Source code |
| CoefToParams | Source code |
| ConcatenateFits | Source code |
| ConvertToSingleDay | Source code |
| CumSumLeftRight | Source code |
| CumSumTrans | Source code |
| CutoffMap | Source code |
| DatLongToEnvironment | Source code |
| DelF.DelI | Source code |
| DelFA.DelI | Source code |
| DelFB.DelI | Source code |
| DelPhi.Dela | Source code |
| DelPhi.Delb | Source code |
| DelR.Dela | Source code |
| DelR.Delb | Source code |
| DeseqNormalizeLong | Source code |
| DiffPhase | Source code Source code |
| DoChowTest | Source code |
| DoDESEQ | Source code |
| DoFourier | Source code |
| DoFourier.se | Source code |
| EnsemblGene2Gene | Source code |
| FilterCombos | Source code |
| FilterForPeaks | Source code |
| FilterModelByAmp | Source code |
| FilterSingleBait | Source code |
| FilterTADs | Source code |
| FindPeaks | Source code |
| FitCombinations | Source code |
| FitExpDecay | Source code |
| FitLinear | Source code |
| FitModel | Source code |
| FitModels | Source code |
| FitRhythmAcrossFrags | Source code |
| FitRhythmRegion | Source code |
| FitRhythmicAssays | Source code |
| FitRhythmicDesMat | Source code |
| FitToMat | Source code |
| FormatAndFitRhythmAcrossFrags | Source code |
| FormatDat | Source code |
| GePhaseFromParams | Source code |
| Gene2Ensembl | Source code |
| Gene2StartEnd | Source code |
| Gene2Strand | Source code |
| GetAdeltSigDelt | Source code |
| GetAllCombos | Source code |
| GetAmpPhaseFromActivities | Source code |
| GetAvgAmpFromParams | Source code |
| GetAvgFirstDeriv | Source code |
| GetBadSamples | Source code |
| GetBaitLocations | Source code |
| GetBaitLocations2 | Source code |
| GetBestModel | Source code |
| GetCosCombos | Source code |
| GetCyclixRegions | Source code |
| GetDeltaSubLst | Source code |
| GetDesignMatrices | Source code |
| GetEigens | Source code |
| GetFlatModel | Source code |
| GetFourierEntropy | Source code |
| GetIndexOfNoisyFrags | Source code |
| GetInterval | Source code |
| GetMaxPhaseDiffFromParams | Source code |
| GetNextFrag | Source code |
| GetNextFragRange | Source code |
| GetNoiseFactor | Source code |
| GetNrhythFromModel | Source code |
| GetOmegas | Source code |
| GetPeakWidth | Source code |
| GetRegion | Source code |
| GetRegionFromLab | Source code |
| GetRegions | Source code Source code |
| GetRegionsMatchBait | Source code |
| GetRhythModel | Source code |
| GetRhythModel.cos | Source code |
| GetRhythModel.sin | Source code |
| GetRhythmicFormula | Source code |
| GetRhythmicFormula.Shared | Source code |
| GetRightLeftLimits | Source code |
| GetSampIndex | Source code |
| GetSampleNumber | Source code |
| GetSdPhaseFromParams | Source code |
| GetSelectionCriterion | Source code |
| GetSeriesFromSampi | Source code |
| GetSinCombos | Source code |
| GetSlopes | Source code |
| GetSlopes.trans | Source code |
| GetTopNModelsFromFits | Source code |
| HandleNAs | Source code |
| HexColorToRgb | Source code |
| IsRhythmic | Source code |
| IsSignif | Source code |
| IsSignif2 | Source code |
| LabelSignifHits | Source code |
| ListToLong | Source code |
| LoadAssayZscores | Source code |
| LoadBed | Source code |
| LoadChunkRunNconds | Source code |
| LoadDataset | Source code |
| LoadDesMatDatGeneRunFits | Source code |
| LoadExonIntronCounts | Source code |
| LoadFitsFromModels | Source code |
| LoadRobjPlotSummary | Source code |
| MakeDesMatChunks | Source code |
| MakeDesMatFromModelName | Source code |
| MakeDesMatRunFit | Source code |
| MakeDesMatRunFitEnv | Source code |
| MakeGenotypeLabeller | Source code |
| MakeHash | Source code |
| MakeModelName | Source code |
| MakeRhythmicDesignMatrices | Source code |
| MakeSampNames | Source code |
| MaxDiffPhaseVector | Source code |
| MergeCounts | Source code |
| MergeCountsLivKid | Source code |
| MergeCountsLivKidTemporal | Source code |
| MergeCountsWTKO | Source code |
| MergeZscoreAndZscoreKO | Source code |
| NRhythmicFromString | Source code |
| NRhythmicFromVector | Source code |
| NormalizeComplexMat | Source code |
| NormalizeWeights | Source code |
| NormalizeWeightsFromFits | Source code |
| OrderAroundZero | Source code |
| OrderCisFragments | Source code |
| OrderDecreasing | Source code |
| PhaseAmpPvalToColor | Source code |
| PhaseDelta | Source code |
| PlotAmpZscore4C | Source code |
| PlotAmps4C | Source code |
| PlotComponentOriginal | Source code |
| PlotDelta | Source code |
| PlotDeltaLKLR | Source code |
| PlotDeltaLR | Source code |
| PlotEncodeRnaseq | Source code |
| PlotGeneAcrossTissues | Source code |
| PlotGeneAcrossTissuesRnaseq | Source code |
| PlotGeneLivKidKO | Source code |
| PlotGeneNormalized | Source code |
| PlotGeneTissuesWTKO2 | Source code |
| PlotPeriodogramLong | Source code |
| PlotPval | Source code |
| PlotPvalChiSqr | Source code |
| PlotPvalLK | Source code |
| PlotPvalLKLR | Source code |
| PlotPvalLR | Source code |
| PlotPvalLR.geno | Source code |
| PlotPvaluesOverlay | Source code |
| PlotQuad | Source code |
| PlotRnaseq | Source code |
| PlotRnaseqAcrossTissues | Source code |
| PlotSignal | Source code |
| PlotSignalDelta | Source code |
| PlotSignalDeltaLR | Source code |
| PlotSignalLR | Source code |
| PlotSignalLR.WTKOMerged | Source code |
| PlotSignalLR.geno | Source code |
| PlotSignalLR2 | Source code |
| PlotSignalLivVsKid | Source code |
| PlotSignalLivVsKidLR | Source code |
| PlotSignalOverTime | Source code |
| PlotSignalWithHeatmap | Source code |
| PlotTpmAcrossTissues | Source code |
| PlotTriple | Source code |
| PlotVolcano | Source code |
| PlotYOverTime | Source code |
| PlotZscorePval | Source code |
| PlotZscorePvalLR | Source code |
| PlotZscorePvalLR2 | Source code |
| PlotZscoresOverlay | Source code |
| Project4CtoZscore | Source code |
| ProjectOnVector | Source code |
| ProjectToFrequency | Source code |
| ProjectToFrequency2 | Source code |
| ProjectWithZscore | Source code |
| PutPosInBin | Source code |
| PutPosInBin.cistrans | Source code |
| RemoveFragments | Source code |
| RemoveSample | Source code |
| SaturationCurve | Source code |
| SaveChunk | Source code |
| SaveDatGenes | Source code |
| SeriesToGeno | Source code |
| SeriesToTime | Source code |
| SetWidthLimit | Source code |
| SetYXMaxDelta | Source code |
| SlidingWindowLinReg | Source code |
| SplitPosIntoRegions | Source code |
| StepCurve | Source code |
| StrToCond | Source code |
| SubsetFullDesignMatrix | Source code |
| SumAroundFrags | Source code |
| SumAroundFragsLong | Source code |
| SumWeights | Source code |
| SvdOnComplex | Source code |
| TemporalToFrequency | Source code |
| TemporalToFrequency2 | Source code |
| TemporalToFrequencyDatLong | Source code |
| Transcript2Gene | Source code |
| Transcript2Strand | Source code |
| Transform | Source code |
| UnzipMatrices | Source code |
| UpdateFitWeights | Source code |
| VolcanoPlot | Source code |
| WriteBed | Source code |
| WriteBedGraph | Source code |
| WriteToFile | Source code |
| asinh_trans | Source code |
| bToKb | Source code |
| dequeue | Source code |
| enqueue | Source code |
| expandingList | Source code |
| f | Source code |
| geneRanges | Source code Source code |
| genomicRangesToBed | Source code |
| hello | Man page |
| is.empty | Source code |
| linkedList | Source code |
| multiplot | Source code |
| my_line | Source code |
| my_line_custom | Source code |
| my_line_nolabels | Source code |
| new.queue | Source code |
| panel.cor | Source code |
| panel.hist | Source code |
| pseudoLog10 | Source code |
| scale1decimal | Source code |
| scale2decimal | Source code |
| scatter_with_xy_line | Source code |
| scientific_10_posexpo | Source code |
| splitColumnByOverlap | Source code Source code |
