API for jakeyeung/scchic-functions
| Global functions | |
|---|---|
| .modelMatSelection | Source code |
| AddCellCycleLabel | Source code |
| AddCellCycleLabel.bydat | Source code |
| AddGeneNameToRows | Source code |
| AddPlateCoordinates | Source code |
| AddTopicToTmResult | Source code |
| AdjustBatchEffect | Source code |
| AdjustBatchEffect2 | Source code |
| AnnotateBins | Source code |
| AnnotateBins2 | Source code Source code |
| AnnotateCoordsFromList | Source code |
| AnnotateCoordsFromList.GeneWise | Source code |
| AnnotateRegionToGene | Source code |
| AnnotateSortFromLayout | Source code |
| AnnotateSortFromLayout.dat | Source code |
| AnnotateSortFromLayout.rep2 | Source code |
| AnnotateSortFromLayoutBMall | Source code |
| AnnotateTermsToNearestGene | Source code |
| ApplyAcrossClusters | Source code |
| AssignEffect | Source code |
| AssignEffect2 | Source code |
| BatchColumn2Ctype | Source code |
| BinTrajectory | Source code |
| BinarizeMatrix | Source code |
| CalculateACF | Source code |
| CalculateCumSumNegCor | Source code |
| CalculateEntropy | Source code |
| CalculateVarAcrossChromo | Source code |
| CalculateVarAll | Source code |
| CalculateVarRaw | Source code |
| CalculateVarTotal | Source code |
| CalculateVarWithinChromo | Source code |
| ChooseBestLDA | Source code |
| CleanCoords | Source code |
| ClipLast | Source code |
| ColNorms | Source code |
| CollapseMatByLouvains | Source code |
| CollapseRowsByGene | Source code |
| CollapseTaggedCountCnames | Source code |
| ColorsByCounts | Source code |
| ColorsByGamma | Source code |
| DoLeiden | Source code |
| DoLouvain | Source code |
| DoUmapAndLouvain | Source code |
| DoUmapFromLDA | Source code |
| FilterBinsByBlacklist | Source code |
| FitGetPval | Source code |
| FitGlmRowChromocounts | Source code |
| FitGlmRowClusters | Source code |
| FitGlmRowClustersPlate | Source code |
| FitGlmRowClustersPlate.withse | Source code |
| FitGlmRowRaw | Source code |
| FitGlmRowSpikeins | Source code |
| FitLmRowChromocounts | Source code |
| FitLmRowSpikeins | Source code |
| FitMixingWeight | Source code |
| FitMixtureModelLabelCells | Source code |
| FitMultinoms | Source code |
| FitMultinomsFn | Source code |
| FitNormCountsToNcells.glm | Source code |
| FitNormCountsToNcells.lm | Source code Source code |
| FitNormCountsToNcells.lm.naive | Source code |
| FitSlope | Source code |
| FixMarkName | Source code |
| FixMarkName2 | Source code |
| GetArrows | Source code |
| GetBedFromCoords | Source code |
| GetBins | Source code |
| GetCellGastru | Source code |
| GetCellHashBC | Source code |
| GetCellSd | Source code |
| GetCellsAlongTraj | Source code |
| GetChromo | Source code |
| GetChromoCounts | Source code |
| GetCondFromSamp | Source code |
| GetCondFromSamp.blood | Source code |
| GetCors | Source code |
| GetCountMatFromLDA | Source code |
| GetCrit | Source code |
| GetDiffRelToCell | Source code |
| GetDiffRelToCell2 | Source code |
| GetDoubleName | Source code |
| GetEmptyWells | Source code |
| GetEnd | Source code |
| GetFACSloadings | Source code |
| GetGOData | Source code |
| GetGeneAnnotsHash | Source code |
| GetGeneCounts | Source code |
| GetGeneSets | Source code |
| GetK9CelltypeBins | Source code |
| GetLLMerged | Source code |
| GetLengthTime | Source code |
| GetMarkFromStr | Source code |
| GetMarkGastru | Source code |
| GetMatSub | Source code |
| GetNMarks | Source code |
| GetParamsWideFormat | Source code |
| GetPeakSize | Source code |
| GetPeaksFromGene | Source code |
| GetPlateCoord | Source code |
| GetPlateCoord2 | Source code |
| GetPlateWellFromRowCol | Source code |
| GetRefCnames | Source code |
| GetRepBM | Source code |
| GetRepGastru | Source code |
| GetStage | Source code |
| GetStart | Source code |
| GetStrain | Source code |
| GetTime | Source code |
| GetTmResultFromGensim | Source code |
| GetTrajSum | Source code |
| GetUmapSettings | Source code |
| GetVar | Source code |
| GetWKMgenes | Source code |
| GetWellPosition | Source code |
| GrepAndWriteMat | Source code |
| HasG1 | Source code |
| HellingerDistance | Source code |
| HexPlot | Source code |
| InitGLMPCAfromLDA | Source code |
| InverseDocFreq | Source code |
| IsRound1 | Source code |
| KeepLast | Source code |
| L2Norm | Source code |
| LabelMetadataByCtype | Source code |
| LoadBlacklist | Source code |
| LoadCellAnnots | Source code |
| LoadCellAnnotsEtOH | Source code |
| LoadCellAnnotsEtOH.MorePlates | Source code |
| LoadFACS | Source code |
| LoadFACSGetLoadings | Source code |
| LoadGetImputed | Source code |
| LoadGetTmResult | Source code |
| LoadLDA | Source code |
| LoadLDABins | Source code |
| LoadMARA | Source code |
| LoadMats | Source code |
| LoadUmap | Source code |
| MakeLowerPlot | Source code |
| MakeVariabilityPlots | Source code |
| MarkerToCelltype | Source code |
| MatToLong | Source code |
| MergeSdWithPseudotime | Source code |
| MergeVarWithinAcross | Source code |
| MultinomFitsToLong | Source code |
| MultinomFitsToLong.percell | Source code |
| Norm | Source code |
| NormalizeMatrix | Source code |
| NormalizeMatrix2 | Source code |
| OrderTopicsByEntropy | Source code |
| ParseCoord | Source code |
| PlotAllMarks | Source code |
| PlotDecreasingWeights | Source code |
| PlotMotifInUmap | Source code |
| PlotPseudobulkZscore | Source code |
| PlotSpatialGene | Source code |
| PlotXYNoColor | Source code |
| PlotXYWithColor | Source code |
| PreprocessSamp | Source code |
| RankOrder | Source code |
| ReadChrReads | Source code |
| ReadDinuc | Source code |
| ReadDinucGastru | Source code |
| ReadLH | Source code |
| ReadLH.SummarizeTA | Source code |
| ReadMatSlideWinFormat | Source code |
| ReadMatTSSFormat | Source code |
| ReadRZ | Source code |
| RefitPoissonForPlot | Source code |
| RunLSI | Source code |
| RunLSI2 | Source code |
| SelectBestPeak | Source code |
| SelectTopRegions | Source code |
| SetUpProbs | Source code |
| SoftMax | Source code |
| SplitGetLast | Source code |
| StageToNumeric | Source code |
| StrToBool | Source code |
| StrToNA | Source code |
| StrToNumeric | Source code |
| StrToVector | Source code |
| SumAcrossChromos | Source code |
| SumAcrossClusters | Source code |
| SumSqrDev | Source code |
| SummarizeACF | Source code |
| SummarizeMeanValue | Source code |
| SummarizeMultinomFits | Source code |
| SummarizeParamsPvalues | Source code |
| SwapTechRep | Source code |
| SwitchColnames | Source code |
| TermFreq | Source code |
| TermFreq2 | Source code |
| TidyMixtureModelOutputs | Source code |
| TotalVar | Source code |
| UmapLSIOutput | Source code |
| UnmixRawCounts | Source code |
| UpdateW | Source code |
| args.to.numeric | Source code |
| binomial_deviance | Source code |
| binomial_deviance_residuals | Source code |
| cbind.fill.lst | Source code |
| center.cols | Source code |
| center.rows | Source code |
| compute.lml | Source code |
| compute_size_factors | Source code |
| fast.svd | Source code |
| fit.promoter.scale | Source code |
| gof_func | Source code |
| hello | Man page Source code |
| jCanonCor | Source code |
| jMultiCCA | Source code |
| l2n | Source code |
| l2norms.frac | Source code |
| multinomial_deviance | Source code |
| null_residuals | Source code |
| optimize.lambda | Source code |
| poisson_deviance | Source code |
| poisson_deviance_residuals | Source code |
| read.table.handlerows | Source code |
| ridge.regression | Source code |
| ridge.regression.qr | Source code |
| target.prediction | Source code |
| variable.selection | Source code |
