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
jakeyeung/Circadian4Cseq documentation built on Dec. 1, 2019, 2:57 a.m.