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 |
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