API for jakeyeung/TissueCiradianAnalysis
Analysis of oscillatory RNASeq data
| Global functions | |
|---|---|
| AICFromLmFit | Source code |
| AcosBsinToAmpPhase | Source code |
| AddAlphaToHexColor | Source code |
| AddColname | Source code |
| AddDf | Source code |
| AddRhythmicColumns | Source code |
| AddToEnviron | Source code |
| AddX | Source code |
| AdjustArrayToRnaSeq | Source code |
| AdjustPhase | Source code |
| AnalyzeGeneEnrichment | Source code |
| AnnotatePseudogenes | Source code |
| AnnotateTranscriptLength | Source code |
| AppendGeneID | Source code |
| AssignSitecount | Source code |
| Attribute2Gene | Source code |
| AvgAcrossTranscripts | Source code |
| AvgExprsAcrossTissues | Source code |
| BICFromLmFit | Source code |
| BICWeight | Source code |
| BoxplotLdaOut | Source code |
| CalculateDistance | Source code |
| CalculateFractionIsoformUsage | Source code |
| CalculateGaussianCenters | Source code |
| CalculateGaussianDists | Source code |
| CalculatePeriodogram | Source code |
| CalculatePeriodogramLong | Source code |
| CapitalizeFirstLetter | Source code |
| Center | Source code |
| ChunkDatGenesToFile | Source code |
| Cnames | Source code |
| Cnames.long | Source code |
| CoefToModelName | Source code |
| CoefToParams | Source code |
| CollapseDat | Source code |
| CollapseTissueGeno | Source code |
| ConcatenateFits | Source code |
| ConstrainedFitWithNoise | Source code |
| ConvertArgToPhase | Source code Source code |
| ConvertEntrez2Sym | Source code |
| ConvertGO2Entrez | Source code |
| ConvertLongToWide | Source code |
| ConvertRNASeqTissueNamesToArray | Source code |
| ConvertSym2Entrez | Source code |
| ConvertToSingleDay | Source code |
| CoordToBed | Source code |
| CopyZT0ToZT24 | Source code |
| CorrelateAmpPromMulti | Source code |
| CountDistFromMotif | Source code |
| CountModels | Source code |
| CreateEntrez2GO | Source code |
| CreateEntrez2Sym | Source code |
| CreateGO2AllEntrez | Source code |
| CreateGO2Entrez | Source code |
| CreateSym2Entrez | Source code |
| CrossProduct | Source code |
| CrossProductCnames | Source code |
| CrossProductTwoSets | 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 |
| DiffPhase | Source code |
| DoCanCor | Source code |
| DoFourier | Source code |
| DoFourier.se | Source code |
| DoLdaPromoters | Source code |
| DuplicateCnames | Source code |
| EnrichmentBinnedToFile | Source code |
| EnsemblGene2Gene | Source code |
| ExtraParamsFromFit | Source code |
| FTestSigmoidLinearModels | Source code |
| FactorToHex | Source code |
| Filter33Motifs | Source code |
| FilterBedFile | Source code |
| FilterCombos | Source code |
| FilterGenesByTissue | Source code |
| FilterKidneyLiverGenes | Source code |
| FilterLiverGenes | Source code |
| FilterModelByAmp | Source code |
| FilterReadcounts | Source code |
| FilterSignal | Source code |
| FindCutoff | Source code |
| FindCutoff2 | Source code |
| FindCutoffLong | Source code |
| FindMaxFreqs | Source code |
| FindMostRhythmic | Source code |
| FirstColToRowname | Source code |
| FisherTestSitecounts | Source code |
| FitCombinations | Source code |
| FitDfToMatrix | Source code |
| FitLmConstraint | Source code |
| FitLmConstraint2 | Source code |
| FitModel | Source code |
| FitModels | Source code |
| FitMotifAmp | Source code |
| FitPosNeg | Source code |
| FitRhythmic | Source code |
| FitRhythmicDatLong | Source code |
| FitRhythmicDesMat | Source code |
| FitRhythmicScanPeriods | Source code |
| FitRhythmicWeighted | Source code |
| FitRhythmicWeighted.singleintercept | Source code |
| FitSaturationCurve | Source code |
| FitSaturationCurveFindProblemGenes | Source code |
| FitToMat | Source code |
| FixColname | Source code |
| FixColnamesForMARA | Source code |
| FixGeneName | Source code |
| FixRikGenes | Source code |
| FoldChangeRhyth | Source code |
| FracVarByGeneList | Source code |
| FuzzyDistance | Source code |
| GammaMixmdl | Source code |
| Gene2Ensembl | Source code |
| Gene2StartEnd | Source code |
| Gene2Strand | Source code |
| GetActSvd | Source code |
| GetAllCombos | Source code |
| GetAmpPhaseFromActivities | Source code |
| GetAmpRelToMax | Source code |
| GetAvgAmpFromParams | Source code |
| GetBayesFactor | Source code |
| GetBestModel | Source code |
| GetClockGenes | Source code |
| GetCoord | Source code |
| GetCosCombos | Source code |
| GetDensity | Source code |
| GetDesignMatrices | Source code |
| GetESubDir | Source code |
| GetEigens | Source code |
| GetEnrichment | Source code |
| GetEnrichmentOverBins | Source code |
| GetEnrichmentParallel | Source code |
| GetExperiments.merged | Source code |
| GetExprsMat | Source code |
| GetExprsMean | Source code |
| GetFlatModel | Source code |
| GetFourierEntropy | Source code |
| GetFragLength | Source code |
| GetFullR | Source code |
| GetGOEnrichment | Source code |
| GetGONames | Source code |
| GetGeneListAndOrder | Source code |
| GetGeneModelKeys | Source code |
| GetGenesFromMotifs | Source code |
| GetGoObject | Source code |
| GetHistCounts | Source code |
| GetIndex | Source code |
| GetInterval | Source code |
| GetMaxDist | Source code |
| GetMaxPhaseDiffFromParams | Source code |
| GetMeanVarByTissues | Source code |
| GetMergedColnames | Source code |
| GetMinCor | Source code |
| GetMinPeriod | Source code |
| GetMinPeriodSsqResiduals | Source code |
| GetMotifFromGene | Source code |
| GetMotifMat | Source code |
| GetMouseMart | Source code |
| GetNoiseFactor | Source code |
| GetNrhythFromModel | Source code |
| GetOmegas | Source code |
| GetOrderedPeaks | Source code |
| GetPeakDistance | Source code |
| GetPeakwidth | Source code |
| GetPeriodogramFreq | Source code |
| GetPhaseDiff | Source code |
| GetPhaseFromParams | Source code |
| GetPromoterUsage | Source code |
| GetPromoterUsageMaxDist | Source code |
| GetRSquaredFromFits | Source code |
| GetRelamp | Source code |
| GetRhythModel | Source code |
| GetRhythModel.cos | Source code |
| GetRhythModel.sin | Source code |
| GetRhythmic | Source code |
| GetRhythmicFormula | Source code |
| GetRhythmicFormula.Shared | Source code |
| GetRhythmicOrNot | Source code |
| GetRowIndx | Source code |
| GetSdPhaseFromParams | Source code |
| GetSelectionCriterion | Source code |
| GetSinCombos | Source code |
| GetSinusoid | Source code |
| GetSuffix | Source code |
| GetTFs | Source code |
| GetTcdCnames | Source code |
| GetTcdCnames.partial | Source code |
| GetTimes | Source code Source code |
| GetTimes.merged | Source code |
| GetTimesTissuesGenoKL | Source code |
| GetTissSpecPeaks | Source code |
| GetTissueNames | Source code Source code Source code |
| GetTissueSpec | Source code |
| GetTissueSpecific | Source code |
| GetTissueSpecificMatrix | Source code |
| GetTissues | Source code |
| GetTissues.merged | Source code |
| GetTissuesFromCoefFit | Source code |
| GetTopGenesByPeriod | Source code |
| GetTopGenesFromSvd | Source code |
| GetTopMotifs | Source code |
| GetTopNModelsFromFits | Source code |
| GetTopNValues | Source code |
| GetUnobsObsSymbol | Source code |
| GetWeightsFromVar | Source code |
| GrepRikGenes | Source code |
| HellingerDistance | Source code |
| HexColorToRgb | Source code Source code |
| HitOrNot | Source code |
| InitCoeffMat | Source code |
| InvGamma | Source code |
| Is.RhythmicAcrossTissues | Source code |
| Is.TissueSpecific | Source code |
| IsDouble | Source code |
| IsRhythmic | Source code |
| IsRhythmic2 | Source code |
| IsRnaseq | Source code |
| IsSignalLower | Source code |
| IsSignalUpper | Source code |
| IsTissSpec | Source code |
| IsTissueSpecific2 | Source code |
| IsTissueSpecificDplyr | Source code |
| IsTissueSpecificLong | Source code |
| KeepUpToThres | Source code |
| KsTestPosNeg | Source code |
| LaplaceApprox | Source code |
| ListToLong | Source code |
| LmGeneTissue | Source code |
| LoadActivitiesLong | Source code |
| LoadActivitiesLongDhs | Source code |
| LoadActivitiesLongKidneyLiver | Source code |
| LoadActivitiesPlotSvd | Source code |
| LoadArray | Source code |
| LoadArrayRnaSeq | Source code |
| LoadChunkRunNconds | Source code |
| LoadDesMatDatGeneRunFits | Source code |
| LoadEnsemblToPromoter | Source code |
| LoadFitsFromModels | Source code |
| LoadKallisto | Source code |
| LoadKallistoGene | Source code |
| LoadKallistoMerged | Source code |
| LoadLivKid | Source code |
| LoadLong | Source code |
| LoadNormalizedArray | Source code |
| LoadPhosphoData | Source code |
| LoadPol2Activities | Source code |
| LoadPol2Activities.all | Source code |
| LoadProteomicsData | Source code |
| LoadRnaSeq | Source code |
| LoadSitecounts | Source code |
| LoadSitecountsEncode | Source code |
| LoadSitecountsEncodeAll | Source code |
| LoadSitecountsPromotersLong | Source code |
| LongToMat | Source code Source code |
| LongToMat.lda | Source code |
| LoopCor | Source code |
| MakeCluster | Source code |
| MakeCnamesLivKidWTKO | Source code |
| MakeDesMatChunks | Source code |
| MakeDesMatFromModelName | Source code |
| MakeDesMatRunFit | Source code |
| MakeDesMatRunFitEnv | Source code |
| MakeHash | Source code |
| MakeModelName | Source code |
| MakeRhythmicDesignMatrices | Source code |
| MatchColumns | Source code |
| MatchGroup | Source code |
| MaxDiffPhaseVector | Source code |
| MeanCenterAcrossGroups | Source code |
| MeanMat | Source code |
| MergeAndProject | Source code |
| MergeGOTerms | Source code |
| MergeToLong | Source code |
| MixtureDensity | Source code |
| MixtureDensity3 | Source code |
| Mode | Source code |
| ModeG | Source code |
| ModelLikelihood | Source code |
| ModelLikelihood2 | Source code |
| ModelRhythmicity | Source code |
| ModelStrToModel | Source code |
| ModelToTissue | Source code |
| NGenesByAmp | Source code |
| NGenesByAmp.long | Source code |
| NRhythmicFromString | Source code |
| NRhythmicFromVector | Source code |
| Normalize | Source code |
| NormalizeComplexMat | Source code |
| NormalizeWeights | Source code |
| NormalizeWeightsFromFits | Source code |
| NrhythToStr | Source code |
| OrderDecreasing | Source code Source code |
| OrderPhaseMatrix | Source code |
| OuterComplex | Source code |
| PCbiplot | Source code Source code |
| PcToMotif | Source code |
| Peek | Source code |
| PenalizedLdaLong | Source code |
| PhaseAmpPvalToColor | Source code Source code |
| PlotActivitiesWithSE | Source code |
| PlotActivitiesWithSE.dhs | Source code |
| PlotActivitiesWithSE.rnaseq | Source code |
| PlotActivitiesWithSE.wtko | Source code |
| PlotAgainstRnaSeq | Source code |
| PlotAmpPhase | Source code |
| PlotAmpPhaseAllTissues | Source code |
| PlotAmpPhaseTissue | Source code |
| PlotArgsMatrix | Source code |
| PlotBeforeAfter | Source code |
| PlotComplex | Source code |
| PlotComplex2 | Source code |
| PlotComplex2.act | Source code |
| PlotComplexCircle | Source code |
| PlotComplexLong | Source code |
| PlotComponentOriginal | Source code |
| PlotComponents | Source code |
| PlotComponents2 | Source code |
| PlotDAGGraph | Source code |
| PlotDiagnostics | Source code Source code Source code |
| PlotDiagnostics2 | Source code |
| PlotDifferentialSitecounts | Source code |
| PlotEigengene | Source code Source code |
| PlotEigensamp | Source code Source code |
| PlotEncodeRnaseq | Source code |
| PlotEnrichmentGenes | Source code |
| PlotExprsHeatmap | Source code |
| PlotFirstNComponents | Source code |
| PlotFitDiagnostics | Source code |
| PlotFitTwoPeriods | Source code |
| PlotGOTermsPhase | Source code |
| PlotGammaDist | Source code |
| PlotGammaMixmdl | Source code |
| PlotGeneAcrossTissues | Source code |
| PlotGeneAcrossTissuesRnaseq | Source code |
| PlotGeneByRhythmicParameters | Source code |
| PlotGeneModuleWithGO | Source code |
| PlotGeneNormalized | Source code |
| PlotGeneTissuesWTKO | Source code |
| PlotGeneTpm | Source code |
| PlotGenesInModel | Source code |
| PlotHeatmapAmpPhasePval | Source code |
| PlotHeatmapGeneList | Source code |
| PlotHeatmapNconds | Source code |
| PlotLdaOut | Source code |
| PlotLdaOut2D | Source code |
| PlotLoadings | Source code Source code |
| PlotMeanActivitiesWithSE | Source code |
| PlotMeanActivitiesWithSE.singleintercept | Source code Source code |
| PlotMeanExprsOfModel | Source code |
| PlotOverlayTimeSeries | Source code |
| PlotPCTissue | Source code |
| PlotPeriodogram | Source code |
| PlotPeriodogramLong | Source code |
| PlotPolarHistogram | Source code |
| PlotPromoter | Source code |
| PlotProteomics | Source code |
| PlotRelampHeatmap | Source code |
| PlotRnaMicroarrayFit | Source code |
| PlotRnaseqAcrossTissues | Source code |
| PlotSeparation | Source code |
| PlotSitecounts | Source code |
| PlotSvdFromGeneList | Source code |
| PlotTissuePcaFromGenelist | Source code |
| PlotTpmAcrossTissues | Source code |
| PlotTpmAcrossTissuesWTKO | Source code |
| PlotmRNAActivityProtein | Source code |
| PredictFromMM | Source code |
| PredictFromMM3 | Source code |
| PredictFromMMGamma | Source code |
| PriorG | Source code |
| ProjectActivities | Source code |
| ProjectOnVector | Source code |
| ProjectToFrequency | Source code Source code |
| ProjectToFrequency2 | Source code |
| ProjectToPeriodicTime | Source code |
| ProjectWithZscore | Source code |
| PromAmpScore | Source code |
| PromoterSpacePlots | Source code |
| PromoterSpacePlots.nostics | Source code |
| PvalFromFit | Source code |
| ReadAutocorrelation | Source code |
| ReadDHSData | Source code |
| ReadListToVector | Source code |
| ReadSitecountsMotif | Source code |
| ReadTagCountsDistribution | Source code |
| RemoveCommasBraces | Source code |
| RemoveDashes | Source code |
| RemoveExtension | Source code |
| RemoveLowExprsPseudoShortGenes | Source code |
| RemoveLowlyExpressedGenes | Source code |
| RemoveP2AndCommaBracesDashes | Source code |
| RemoveP2Name | Source code |
| RemoveProblemGenes | Source code |
| RemoveX | Source code |
| ReplaceNegs | Source code |
| RhythTiss | Source code |
| RhythmicOrNot | Source code |
| RnaseqNames | Source code |
| RunElasticNet | Source code |
| RunFisherDHS | Source code |
| RunFisherOnPromoters | Source code |
| RunFuzzyDistance | Source code |
| RunPenalizedLDA | Source code |
| S | Source code |
| S2 | Source code |
| SameTimepointsLivKid | Source code |
| SaturationCurve | Source code Source code |
| SaveChunk | Source code |
| SaveDatGenes | Source code |
| ScaleRemoveInfs | Source code |
| ScaleSignal | Source code |
| ScatterLdaOut2D | Source code |
| SecondDerivG | Source code |
| SetUpMatForLda | Source code |
| SetdiffTimepoints | Source code |
| ShannonEntropy | Source code |
| ShannonEntropyMixMdl | Source code |
| ShortenSampNames | Source code |
| SortByTissue | Source code |
| SortCname | Source code |
| SortLda | Source code |
| StaggeredTimepointsLivKid | Source code |
| StepCurve | Source code |
| SubLongToMat | Source code |
| SubsetAndFishers | Source code |
| SubsetByMaxBicWeight | Source code |
| SubsetFullDesignMatrix | Source code |
| SubsetGenoSignalTimeType | Source code |
| SumWeights | Source code |
| SummarisePeriodogram | Source code |
| SummarisePeriodogram2 | Source code |
| SvdOnComplex | Source code |
| TakeIfSame | Source code |
| TemporalToFrequency | Source code |
| TemporalToFrequency2 | Source code |
| TemporalToFrequencyDatLong | Source code |
| TimeFromCname | Source code |
| TimesNames | Source code |
| TissueFromCname | Source code |
| TissueNames | Source code |
| Transcript2Gene | Source code |
| Transcript2Strand | Source code |
| Transform | Source code |
| UnzipMatrices | Source code |
| UpdateFitWeights | Source code |
| WriteGeneListMat | Source code |
| WriteGeneListMat2 | Source code |
| WriteListToFile | Source code |
| add.alpha | Source code |
| bedToUCSC | Source code |
| cancor.svd | Source code |
| circular_phase24H_histogram | Source code |
| cossim | Source code |
| dequeue | Source code |
| enqueue | Source code |
| expandingList | Source code Source code |
| geneRanges | Source code Source code |
| genomicRangesToBed | Source code |
| gg_color_hue | Source code |
| hello | Man page |
| is.empty | Source code |
| is_outlier | Source code |
| is_top_N | Source code |
| linkedList | Source code Source code |
| lsos | Source code |
| make.block | Source code |
| make_circ_coord | Source code |
| mergePDF | Source code |
| multiplot | Source code |
| new.queue | Source code |
| screenshotUCSC | Source code |
| seg | Source code |
| seg.dp | Source code |
| showSigNodes2 | Source code |
| splitColumnByOverlap | Source code Source code |
| unregister | Source code |
